title: Stationary  cells, assay 3, 15 min

city: Braga

first: Maria Daniela

last: Silva

address: Campus de Gualtar,

department: Centre of Biological Engineering

country: Portugal

institute: University of Minho

data_processing:
CLC Genomics Workbench version 21 (Qiagen) was used for length trimming, mapping to reference genomes and normalization of gene expression. Trimmed reads were aligned to bacteria and phage reference genomes. Gene expression was normalized by calculating Reads per Kilobase per Million Mapped Reads (RPKM). Baggerley’s test was applied to identify statistically significant alterations between different time-points (0 min vs 5, 15, and 30 min post-infection) and cell state (exponential vs stationary cells).
Assembly: Staphylococcus epidermidis RP62A: GenBank accession number CP000029; Staphylococcus phage phiIBB-SEP1: GenBank accession number NC_041928
Supplementary files format and content: xlsx files containing the RPKM values, fold change and FDR adjusted p-value

organism: Staphylococcus epidermidis

growth_protocol: In the case of exponential phase cells, 200 μL of an overnight grown culture of S. epidermidis 9142 were used to inoculate 20 mL of fresh TSB and bacteria allowed to grow at 37 °C, 120 rpm, until an OD600nm of approximately 0.35. In the case of stationary cells, S. epidermidis 9142 was grown for 48 h at 37 °C and 120 rpm. Thereafter, part of the culture was centrifuged (9000 g, 10 min, 4 °C) and the supernatant was used to dilute the remaining cell suspension to an OD600nm of approximately 0.35.

extract_protocol:
Samples for RNA isolation were taken from the non-infected cultures shortly before infection (0 min) and from the infected cultures at 5, 15, and 30 min post-infection. Samples were immediately mixed with a 1:10 volume of an ice-cold stop solution. Total RNA extraction was performed using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions with some modifications. Genomic DNA was degraded using the TURBO DNA-free™ Kit (Thermo Scientific). RNA integrity was determined using the Bioanalyzer 2100 equipment and an RNA 6000 Pico Kit (Agilent Technologies). Samples from three independent experiments with an RNA Integrity Number (RIN) above 8 were selected for RNA-seq.
RNA samples were sent to Novogene (UK) for library preparation and prokaryotic RNA sequencing using the Illumina NovaSeq 6000 Sequencing System (paired-end 150 bp).

treatment_protocol: Cells were infected with phage SEP1 at a multiplicity of infection (MOI) of 5.

tag: strain

tag: cell state

value: stationary

value: Staphylococcus phage phiIBB-SEP1

tag: moi

value: 15 min

tag: assay


title: Stationary  cells, assay 3, 30 min

status: Public on May 15 2024

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: treatment

tag: time

value: 30 min


title: 607-CNTNAP2-KO-AD-F_S12_L002

city: Povo (TN)

first: ENRICO

last: DOMENICI

address: via Sommarive n. 9

department: CELLULAR, COMPUTATIONAL AND INTEGRATIVE BIOLOGY

country: Italy

institute: University of Trento

description:
607-CNTNAP2
S12

data_processing:
Trimming - Alignment and feature count
Trimming with Trim_galore
Alignment with STAR
Feature count with STAR
Assembly: GRCm39.primary_assembly.genome.fa.gz
Supplementary files format and content: Matrix of gene counts

organism: Mus

source_name: cerebella

extract_protocol:
Brain samples used for flow cytometry were homogenized with pestles immediately after dissections and single-cell suspension were generated using Falcon 70 um cell strainer (Corning). After the isolation, brain cells were washed with complete medium and incubated for 12h at 37°C. Total RNAs were extracted from cerebral cerebella of adult Cntnap2 +/+  Cntnap2-/- mice using RNeasy Plus Mini Kit (Qiagen), and retro-transcribed to cDNA according to published protocol.
The quality and the integrity of the RNA samples, RNA Integrity Numbers (RIN) were assessed using a 2100 Bioanalyzer Instrument (Agilent). Only samples with RIN > 8 were considered for the analysis. Libraries were prepared using a TruSeq Stranded mRNA Library Prep (48 Samples) Kit (Illumina). Library preparation, quality check, and sequencing were carried out using Illumina NovaSeq6000.

tag: tissue

value: cerebella

tag: genotype

value: KO

tag: age

value: adult (AD)

tag: Sex

value: F

tag: groups

value: KO-AD-F


title: Stationary cells, assay 3, 5 min

value: 5 min


title: Control MDA-MB-231 Replicate 1

type: RNA

city: Nanjing

first: Wenwen

last: Zhang

state: Jiangsu

address: 68 Changle Road

country: China

institute: Nanjing Medical University

hyb_protocol: Scanned on an Agilent G2565AA scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Homo sapiens

source_name: MDA-MB-231 Cells

label_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

growth_protocol: MDA-MB-231 cells were kept in an undifferentiated, pluripotent state by using 1000 IU/ml leukemia inhibitory factor (LIF; Chemicon, ESGRO, ESG1107), and grown on top of murine embryonic fibroblasts feeder layer inactivated by 10 ug/ml of mitomycin C (Sigma, St. L

extract_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

treatment_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: cell line

value: MDA-MB-231 cell

value: Control


title: 12_LNA2_rep2_72h_S12_LANE1

city: Turku

first: Riitta

last: Lahesmaa

address: Tykistökatu 6A

department: Turku Bioscience

country: Finland

institute: University of Turku

library_source: genomic

data_processing:
Read quality-check and adapter trimming was performed using FastQC (v.0.11.4) (17) and TrimGalore (v. 0.4.5) (https://www.bioinformatics.babraham.ac. uk/projects/trim_galore/), respectively.
The trimmed reads were mapped to the hg38 reference genome using Bowtie2 (v. 2.3.3.1) (23).
Open chromatin regions were identified and quantified using the peak caller MACS2 (v. 2.1.0) (24). MACS2 quantifies the peak signal by calculating a fold enrichment value for the peak summit. against random Poisson distribution with local lambda, which is a dynamic parameter defined for each candidate peak. Local lambda captures the influence of local biases and is robust against occasional low read counts at small local regions.
The regions were annotated using HOMER (v.4.9)
Assembly: hg38
Supplementary files format and content: bigwig and narrow peak

molecule: genomic DNA

source_name: blood

growth_protocol: Ficoll (GE Healthcare, cat# 17-1440-03) was used to isolate PBMCs from human umbilical cord blood samples from Turku University Central Hospital, which was followed by CD4+ T cells were isolation (Invitrogen (cat# 11331D).  CD4+ T cells were activated using a plate coated anti-CD3 antibody (Beckman Coulter, cat# IM-1304), and anti-CD28 antibody (Beckman Coulter, cat# IM1376) was added in X-vivo 20 serum-free medium (Lonza, Bazel, Switzerland) containing 0.5 million cells/mL complemented with L-glutamine (2 mM, Sigma-Aldrich) and antibiotics (50 U/mL penicillin and 50 μg/mL streptomycin; Sigma-Aldrich) was used for the cultures. Cells were plated at a density of 2 million cells per well and cultured at 37° C in 5% CO2.

extract_protocol:
Nuclei were isolated, and the libraries were prepared using Nextera DNA library preparation kit with i7 and i5 indices (15028212). AMPURE-XP beads (B46053, Beckman Coulter) were used to purify the libraries.
All samples were pooled into one pool and sequenced on two lanes.

treatment_protocol: For LNA transfections, 4 million cells mixed with 150 pmols of LNA, prepared in 100 μL volume of OptiMEM (Gibco by Life Technologies, cat # 31985-047), were used to transfect the cells using the Amaxa Nucleofector II system (Lonza). After transfection, cells were first rested at 37° C for 48 h in RPMI 1640 (Sigma-Aldrich) medium supplemented with 10% FCS, 50 U/mL penicillin, 50 μg/mL streptomycin, and 2 mM L-glutamine and then activated and cultured as described above

value: blood

tag: cell type

value: CD4+ T cells

value: LIRIL2R LNA2

value: Activated under iTreg condition for 72 hours


title: Stationary  cells, assay 2, 30 min


title: WT1,FlagMTF2_EH,DoxycyclineRemoval, Flag, Rep2

city: Boston

first: Danesh

last: Moazed

state: MA

address: 240 longwood avenue

department: Cell Biology

country: USA

institute: Harvard Medical School

data_processing:
ChIP-seq reads were quality controlled with fqc (v0.11.5)
Pooled libraries were demultiplexed using fastx.
Reads were aligned to custom reference genome HG19 with a reporter inserted at Chr11 (near WT1reporter coordinates hg19 32460504-32463612) or Chr3 (near TFRC reporter coordinates hg19 195809796-195812888) and Drosophila (dm3) using bowtie2 with default parameters. Bam files were generated with samtools 1.3.1
The mapped reads for H3K27me3 ChIP were normalized to scale factor using Deeptools, and mapped reads for Flag ChIP were normalized to reads per genome content using Deeptools  and saved as bw files and visualized in IGV.
Assembly: HG19 with a reporter inserted at Chr11 (near WT1reporter coordinates hg19 32460504-32463612) or Chr3 (near TFRC reporter coordinates hg19 195809796-195812888) and Drosophila (dm3)
Supplementary files format and content: bigWig

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2. Doxycycline was added at a concentration of 1ug/ml

extract_protocol:
Cells for ChIP were cultured in 15 cm plates (~10 million cells). Cell pellets were first washed with cold PBS, crosslinked at room temperature with 1% formaldehyde (ThermoFisher Scientific) for 8 min. Crosslinking reactions were quenched by addition of 125 mM glycine for 10 min. Cell were then resuspended in Swelling Buffer (25 mM Hepes pH 7.8, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT) followed by Dounce homogenization. Nuclei were pelleted by centrifugation and then resuspended in sonication buffer (0.1% SDS, 1 mM EDTA and 10 mM Tri-HCl pH 8.0). The nuclei were sonicated to shear chromatin into ∼200-500 bp fragments using a Covaris E220. Sonicated samples were diluted with ChIP dilution buffer (0.1% SDS, 1 mM EDTA and 10 mM Tri-HCl pH 8.0, 1% Triton X-100, 150 mM NaCl). Diluted samples were centrifuged at 13,000 rpm for 10 min. The supernatant was used for immunoprecipitation using antibodies and 25 μl protein A/G beads for 12-16 h at 4°C (see Table S9 for antibodies). For H3K27me3 ChIP-Seq, Drosophila S2 chromatin (Active Motif# 53083) and histone H2Av antibody (Active Motif# 61686) were added as spike-in controls. ChIP-Seq samples for Flag antibody do not have spike-in controls. The beads were washed twice with high salt wash buffer A (50 mM Hepes pH 7.9, 500 mM NaCl, 1 mM EDTA, 1% Triton, 0.1% Sodium deoxycholate, and 0.1% SDS), twice with wash buffer B (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% Sodium deoxycholate, 0.5% NP-40) and twice with 1X TE (10 mM Tris-HCl, 1mM EDTA). The bound chromatin fragments were eluted with elution buffer (50 mM Tris pH 8.0, 1 mM EDTA, 50 mM NaHCO3,1% SDS) twice for 10 min each at 65°C. Eluted DNA-proteins complexes were incubated overnight at 65°C to reverse crosslinks. RNAase A followed by Proteinase K was then added to digest RNA and protein. DNA was further purified using phenol chloroform/PCR Purification Kit (QIAGEN)
For ChIP-seq, sequencing library was constructed using TruSeq DNA sample Prep Kits (Illumina) and adapter dimers were removed by 2% agarose and Tris-acetate-EDTA gel  electrophoresis. Size selected and purified DNA libraries were sequenced on an Illumina NextSeq 500 machine (Bauer core facility at Harvard University) to obtain 75 bp single-end reads.

value: Human embryonic kidney

tag: chip antibody

value: Flag (Sigma #F1804)


title: 795-CNTNAP2-WT-AD-F_S1_L002

description:
795-CNTNAP2
S1

value: WT

value: WT-AD-F


title: 11_LNA1_rep2_72h_S11_LANE2

value: LIRIL2R LNA1


title: Stationary cells, assay 2, 5 min

value: stationary

value: Staphylococcus phage phiIBB-SEP1


title: Stationary cells, assay 3, 0 min

value: No treatment

value: 0 min


title: 836-CNTNAP2-WT-AD-F_S5_L002

description:
836-CNTNAP2
S5

value: cerebella

value: adult (AD)

value: F


title: 985-CNTNAP2-WT-AD-F_S3_L002

description:
985-CNTNAP2
S3


title: 11_LNA1_rep2_72h_S11_LANE1


title: Stationary  cells, assay 2, 15 min

value: 15 min


title: WT1,FlagMTF2_EH,DoxycyclineAddition, Flag, Rep1


title: 10_NT_rep2_72h_S10_LANE1

value: blood

value: NT LNA


title: WT1,FlagMTF2_EH,DoxycyclineAddition, Flag, Rep2


title: 561-CNTNAP2-WT-P30-F_S28_L002

description:
561-CNTNAP2
S28

value: Thirty (30) days post-natal (P30)


title: Stationary  cells, assay 1, 30 min

value: 30 min


title: 10_NT_rep2_72h_S10_LANE2

value: CD4+ T cells

value: Activated under iTreg condition for 72 hours


title: Stationary cells, assay 2, 0 min


title: Stationary  cells, assay 1, 15 min


title: WT1,FlagMTF2,DoxycyclineRemoval, Flag, Rep1

value: Human embryonic kidney

value: Flag (Sigma #F1804)


title: 9_LNA2_rep2_24h_S9_LANE1

value: LIRIL2R LNA2

value: Activated under iTreg condition for 24 hours


title: 543-CNTNAP2-WT-P30-F_S27_L002

description:
543-CNTNAP2
S27

value: WT


title: 9_LNA2_rep2_24h_S9_LANE2


title: WT1,FlagMTF2,DoxycyclineRemoval, Flag, Rep2


title: 927-CNTNAP2-KO-P30-F_S37_L002

description:
927-CNTNAP2
S37

value: KO


title: WT1,FlagMTF2,DoxycyclineAddition, Flag, Rep2


title: Stationary cells, assay 1, 0 min

value: stationary

value: No treatment

value: 0 min


title: 8_LNA1_rep2_24h_S8_LANE2

value: LIRIL2R LNA1


title: WT1,FlagMTF2,DoxycyclineAddition, Flag, Rep1


title: 822-CNTNAP2-KO-AD-M_S18_L002

description:
822-CNTNAP2
S18

value: cerebella

value: adult (AD)

value: M

value: KO-AD-M


title: 8_LNA1_rep2_24h_S8_LANE1

value: blood


title: WT1,FlagMTF2_EH,DoxycyclineRemoval, Flag, Rep1


title: 606-CNTNAP2-WT-AD-F_S4_L002

description:
606-CNTNAP2
S4

value: F

value: WT-AD-F


title: 7_NT_rep2_24h_S7_LANE2

value: CD4+ T cells

value: NT LNA


title: WT1,FlagMTF2_EH,DoxycyclineRemoval, H3K27me3, Rep1

value: Human embryonic kidney


title: WT1,FlagMTF2_EH,DoxycyclineRemoval, H3K27me3, Rep2


title: Exponential cells, assay 3, 30 min

value: exponential

value: Staphylococcus phage phiIBB-SEP1

value: 30 min


title: Exponential cells, assay 3, 15 min

value: 15 min


title: 925-CNTNAP2-KO-P30-F_S39_L002

description:
925-CNTNAP2
S39

value: KO

value: Thirty (30) days post-natal (P30)


title: WT1,FlagMTF2_EH,DoxycyclineAddition, H3K27me3, Rep2


title: 7_NT_rep2_24h_S7_LANE1

value: Activated under iTreg condition for 24 hours


title: Stationary cells, assay 1, 5 min

value: stationary

value: 5 min


title: Exponential cells, assay 3, 0 min

value: No treatment

value: 0 min


title: WT1,FlagMTF2,DoxycyclineRemoval, H3K27me3, Rep2


title: Exponential cells, assay 3, 5 min


title: Exponential cells, assay 2, 30 min


title: WT1,FlagMTF2_EH,DoxycyclineAddition, H3K27me3, Rep1


title: 926-CNTNAP2-KO-P30-F_S36_L002

description:
926-CNTNAP2
S36

value: cerebella


title: 928-CNTNAP2-KO-P30-M_S31_L002

description:
928-CNTNAP2
S31

value: M


title: 6_LNA_2_72h_rep1_S6_LANE1

value: blood

value: LIRIL2R LNA2

value: Activated under iTreg condition for 72 hours


title: 5_LNA_1_72h_rep1_S5_LANE2

value: CD4+ T cells

value: LIRIL2R LNA1


title: WT1,FlagMTF2,DoxycyclineRemoval, H3K27me3, Rep1

value: Human embryonic kidney


title: 531-CNTNAP2-WT-P30-M_S20_L002

description:
531-CNTNAP2
S20

value: WT


title: 808-CNTNAP2-KO-AD-F_S11_L002

description:
808-CNTNAP2
S11

value: adult (AD)

value: F

value: KO-AD-F


title: 5_LNA_1_72h_rep1_S5_LANE1


title: WT1,FlagMTF2,DoxycyclineAddition, H3K27me3, Rep2


title: Exponential cells, assay 2, 5 min

value: exponential

value: Staphylococcus phage phiIBB-SEP1


title: 108-CNTNAP2-KO-AD-M_S16_L002

description:
108-CNTNAP2
S16

value: KO

value: KO-AD-M


title: 107-CNTNAP2-WT-AD-M_S9_L002

description:
107-CNTNAP2
S9

value: WT-AD-M


title: 4_LNA_NT_72h_rep1_S4_LANE2

value: NT LNA


title: 6_LNA_2_72h_rep1_S6_LANE2


title: WT1,FlagMTF2,DoxycyclineAddition, H3K27me3, Rep1


title: Exponential cells, assay 1, 30 min

value: 30 min


title: 4_LNA_NT_72h_rep1_S4_LANE1

value: blood


title: WT1,MTF2KO,DoxycyclineRemoval, H3K27me3, Rep2


title: Exponential cells, assay 2, 0 min

value: No treatment

value: 0 min


title: 3_LNA_2_24h_rep1_S3_LANE2

value: CD4+ T cells

value: LIRIL2R LNA2

value: Activated under iTreg condition for 24 hours


title: 930-CNTNAP2-KO-P30-M_S32_L002

description:
930-CNTNAP2
S32

value: cerebella

value: Thirty (30) days post-natal (P30)

value: M


title: 3_LNA_2_24h_rep1_S3_LANE1


title: WT1,MTF2KO,DoxycyclineRemoval, H3K27me3, Rep1

value: Human embryonic kidney


title: 429-CNTNAP2-KO-P30-M_S34_L002

description:
429-CNTNAP2
S34


title: 2_LNA_1_24h_rep1_S2_LANE2

value: LIRIL2R LNA1


title: Exponential cells, assay 1, 15 min

value: exponential

value: Staphylococcus phage phiIBB-SEP1

value: 15 min


title: 824-CNTNAP2-KO-AD-F_S14_L002

description:
824-CNTNAP2
S14

value: KO

value: adult (AD)

value: F

value: KO-AD-F


title: WT1,MTF2KO,DoxycyclineAddition, H3K27me3, Rep2


title: Exponential cells, assay 1, 0 min

value: No treatment


title: Exponential cells, assay 2, 15 min


title: 924-CNTNAP2-WT-P30-F_S26_L002

description:
924-CNTNAP2
S26

value: WT


title: WT1,MTF2KO,DoxycyclineAddition, H3K27me3, Rep1


title: WT1,RING1ABKO,DoxycyclineRemoval, H3K27me3, Rep2


title: 1_LNA_NT_24h_rep1_S1_LANE2

value: blood

value: CD4+ T cells

value: NT LNA


title: Exponential cells, assay 1, 5 min

value: 5 min


title: Deaf1, ChIP, replicate2

city: Cardiff

first: NATHAN

last: HARMSTON

address: Museum Avenue

country: United Kingdom

institute: Cardiff University

data_processing:
Quality control was performed using fastqc v0.11.8.
ChIP-seq reads were aligned to the UCSC mm10 genome using version bwa 0.7.17-r1198-dirty.
Duplicates and unmapped reads were flagged with samblaster version 0.1.24, and removed with sambamba version 0.7.0.
Peaks were called using macs2 v2.1.2 with the significance cut-off q-value <= 0.1.
Peaks were merged and filtered using the idr R package. Only highly reproducible peaks with IDR between 0 and 0.05 (inclusive) were kept.
Assembly: mm10
Supplementary files format and content: narrowPeak file includes peak calls from macs2

organism: Mus musculus

growth_protocol: C2C12 were cultured in DMEM media with 10% FBS and 1x pen/strep under 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 mins. After quenching and cell lysis, chromatin was sheared using  Bioruptor sonicator
Native ChIP-seq

value: Mouse myoblasts

value: anti-Deaf1 (Bethyl Laboratories, #A303-187A)


title: Deaf1, Input, replicate2


title: 968-CNTNAP2-KO-P30-M_S33_L002

description:
968-CNTNAP2
S33

value: cerebella

value: Thirty (30) days post-natal (P30)

value: M


title: WT1,RING1ABKO,DoxycyclineRemoval, H3K27me3, Rep3

value: Human embryonic kidney


title: 46-CNTNAP2-WT-AD-M_S7_L002

description:
46-CNTNAP2
S7

value: WT-AD-M


title: 702-CNTNAP2-KO-AD-F_S13_L002

description:
702-CNTNAP2
S13

value: KO


title: 1_LNA_NT_24h_rep1_S1_LANE1

value: Activated under iTreg condition for 24 hours


title: WT1,RING1ABKO,DoxycyclineRemoval, H3K27me3, Rep1


title: HB-4

city: Guangzhou

first: Zhenhua

last: Luo

state: Guangzhou

address: Number 58, zhongshan er road, Yuexiu,

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Raw RNA-seq data was mapped to human transcriptomes GRCh38 v96 (hg38) using Kallisto (v0.46).
Transcripts per million (TPM) value was quantified by Kallisto.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: V{alpha}7.2+ CD3+ MAIT cells

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (Cat# 74004, Qiagen) following the manufacturer’s instructions. Ribosomal RNA were depleted by using VAHTS DNA Clean Beads (Vazyme)
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq Kit v2 following manufacturer's protocols.

value: V{alpha}7.2+ CD3+ MAIT cells

tag: disease state

value: hepatoblastoma


title: Deaf1, Input, replicate1


title: WT1,RING1ABKO,DoxycyclineAddition, H3K27me3, Rep3


title: 825-CNTNAP2-KO-AD-F_S15_L002

description:
825-CNTNAP2
S15

value: adult (AD)

value: F

value: KO-AD-F


title: Deaf1, ChIP, replicate1


title: 2_LNA_1_24h_rep1_S2_LANE1

value: blood

value: CD4+ T cells

value: LIRIL2R LNA1


title: HB-3

value: WT


title: HB-2


title: WT1,RING1ABKO,DoxycyclineAddition, H3K27me3, Rep2


title: 565-CNTNAP2-WT-P30-F_S29_L002

description:
565-CNTNAP2
S29


title: 797-CNTNAP2-WT-AD-F_S2_L002

description:
797-CNTNAP2
S2

value: WT-AD-F


title: WT1,RING1ABKO,DoxycyclineAddition, H3K27me3, Rep1


title: HB-1


title: WT1,HAEED_3A,DoxycyclineRemoval, H3K27me3, Rep2


title: 537-CNTNAP2-WT-P30-F_S25_L002

description:
537-CNTNAP2
S25

value: cerebella


title: 47-CNTNAP2-WT-AD-M_S8_L001

description:
47-CNTNAP2
S8


title: 802-CNTNAP2-WT-AD-M_S10_L001

description:
802-CNTNAP2
S10


title: WT1,HAEED_3A,DoxycyclineRemoval, H3K27me3, Rep1


title: BA-5

value: biliary atresia


title: WT1,HAEED_3A,DoxycyclineAddition,H3K27me3, Rep2


title: BA-4


title: 503-CNTNAP2-WT-P30-M_S23_L001

description:
503-CNTNAP2
S23

value: Thirty (30) days post-natal (P30)

value: M


title: WT1,HAEED_3A,DoxycyclineAddition,H3K27me3, Rep1, rerun

value: Human embryonic kidney


title: WT1,HAEED_3A,DoxycyclineAddition,H3K27me3, Rep1


title: 604-CNTNAP2-KO-AD-M_S17_L001

description:
604-CNTNAP2
S17

value: KO

value: KO-AD-M


title: BA-3

value: V{alpha}7.2+ CD3+ MAIT cells


title: 544-CNTNAP2-KO-P30-F_S38_L001

description:
544-CNTNAP2
S38


title: BA-2


title: WT1,HAEED,DoxycyclineRemoval, H3K27me3, Rep2


title: 890-CNTNAP2-KO-P30-M_S30_L001

description:
890-CNTNAP2
S30


title: BA-6


title: WT1,HAEED,DoxycyclineRemoval, H3K27me3, Rep1


title: FourS20m [Set2d - 1]

city: Singapore

first: Ying

last: Li

state: --- Select a state ---

address: 14 Medical Dr, Singapore

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
Reads were mapped to S.pombe genome by STAR(version STAR_2.5.4b) with default parameters
featureCounts(Version 1.5.0-p1) generated gene expression
Genome_build: ASM294v2
Supplementary_files_format_and_content: tab-delimited text files include normalized gene expression for each sample.

organism: Schizosaccharomyces pombe

source_name: Yeast cell

growth_protocol: Cells were grown to log phase using YEA media at 30°C.

extract_protocol:
Asynchronous growing log phase cells were collected and lysed using glassbeads and FastPrep-24 homogenizer (MP Biomedicals, Santa Ana, CA). Total RNA was extracted using TRIzol (Thermo Fisher Scientific, Waltham, MA), followed by twice extraction with phenol:chloroform:isoamyl alcohol (25:24:1) and once with chloroform. Samples were subsequently treated with DNase I to eliminate the DNA. RNA-seq was performed by BGI (Shenzhen, China) using an Illumina HiSeqTM 2000 platform (Illumina, San Diego, CA).
cDNA


title: CPEP JCPyV infected, biological replicate 2

city: Providence

first: Sheila

last: Haley

state: RI

address: 70 Ship Street

department: MCB

institute: Brown University

description: Gene expression data from primary human choroid plexus cells, comparing cells infected with human polyomavirus JCPyV after 7 days post-infection compared to unifected control cells

scan_protocol: FS450_0001, followed by scan on Affymetrix 3000 7 G scanner

data_processing: The data were analyzed with the Affymetrix default analysis settings within the Applied Biosystem’s Transcriptome Analysis Console (TAC) Software version 4.0

label: Biotin

source_name: Primary human choroid plexus epithelial cell line, Infected with JCPyV, 7 dpi

label_protocol: Affymetrix WTPlus Expression Kit Protocol, 100 ng total RNA input

growth_protocol: Human choroid plexus epithelial cells were cultured in cell line-specific complete media, as indicated by the manufacturer in a humidified incubator at 37°C with 5% CO2 were cultured in cell line-specific complete media, as indicated by the manufacturer in a humidified incubator at 37°C with 5% CO2

extract_protocol: Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, catalog #74134) according to the manufacturer’s instructions.

treatment_protocol: Cells were plated at (10,000 cells/cm2 in poly-l-lysine–coated) in 6 total T150 flasks. The Mad1/SVEdelta strain of JCPyV was propagated in SVGA cells and purified using cesium chloride as previously described. For the infected samples (n = 3 flasks), cells were grown to 80% confluency and then challenged in serum-free media with cesium chloride–purified JCPyV for 1 hour at 37°C.  Uninfected control cells (n = 3 flasks) were treated exactly the same in the absence of virus. Virus-containing media was then aspirated and infected cultures were maintained for 7 days.

value: central nervous system, choroid plexus

value: JCPyV infection


title: 14_LNA1_rep3_24h_S14_LANE2

value: Activated under iTreg condition for 24 hours


title: RWT0m [WT - 2]

value: wild type


title: 501-CNTNAP2-WT-P30-M_S22_L001

description:
501-CNTNAP2
S22


title: WT1,HAEED,DoxycyclineAddition, H3K27me3, Rep2


title: RS20m [Set2d - 2]


title: H128 cells, siERRG3

first: Hong

last: Wang

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

institute: Sun Yat-sen University

data_processing:
sample1-3:single sequencing was performed with Illumina HiSeq 3000 (RiboBio Co, Ltd). TopHat2 and HTSeq were used for RNA-seq data analysis with GRCh38/hg19 as the reference genome. Differential analysis of the RNA-seq data was performed using DESeq2 analysis.
Assembly: hg38
Supplementary files format and content: sample1-3:tab-delimited text files include TPM values for each Sample

source_name: Homo sapiens

growth_protocol: SCLC cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
sample1-3:Total RNA was isolated using TRIzol reagent according to the manufacturer’s instruction (15596026, Invitrogen, USA).
sample1-3:DNase I was used for column digestion to ensure RNA quality. RNA library preparation was performed using the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (E7420L). RNA libraries were prepared for paired-end sequencing using standard Illumina protocols.

treatment_protocol: H128 cells were treated with DN200434 for 48 h or transfected with ERRG siRNA or vehicle siRNA for 48 h.

value: Homo sapiens

value: tumor cells


title: MATR3 KO #5 rep1

city: Bethesda

first: Stefan

last: Muljo

state: MD

address: 10 Center Drive

institute: NIH, NIAID

data_processing:
Reads were mapped to hg38 by STAR version 2.5.2a (PMID: 23104886), allowing for multimapping (parameters –outFilterMultimapNmax 100 –winAnchorMultimapNmax 100)
The expression levels of all genes and TEs were quantified by TEToolkit (PMID: 26206304).
Differential expression was determined by DESeq2 version 1.22.2 (PMID: 25516281), using genes with an average of more than 4 reads per sample.
Gene Set Enrichment Analysis was performed by GSEA(v 4.2.3) (PMID: 16199517) with Hallmarks gene sets (v 2022.1), default parameters.
Assembly: hg38
Supplementary files format and content: Excel file contains Raw Counts, DESeq normalized counts, and DESeq differential expression results comparing the MATR3 KO to the HAP1 WT samples.

growth_protocol: HAP1 cells were cultured in IMDM medium (Quality Biological, cat# 112-035-101) supplemented with 10% (vol/vol) heat-inactivated fetal calf serum (Gibco, cat# 26170-043), 100 U/mL penicillin, 100 µg/mL streptomycin (Gibco, cat# 15140-122), at 37° C in a humidified incubator containing 5% CO2.

extract_protocol:
HAP1 WT and MATR3 KO cells were lysed by RNAzol (Sigma, cat#R4533-100ML??) to prepare total RNA for sequencing using the DirectZol RNA miniPrep Plus (ZYMO RESEARCH, CAT#R2072) per manufacturer’s instruction.
cDNA libraries were prepared with the NEBNext® rRNA Depletion Kit v2  (NEB, E7405L) followed by NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina ( NEB, E7760L) and NEBNext® Multiplex Oligos for Illumina (Unique Dual Index UMI Adaptors RNA Set 1) (E7416L). The final library were sequenced on Novaseq6000, Chemistry 1.5V as 100-8-8-100 at the Genomic  Technology Section, NIAMS, NIH.

treatment_protocol: MATR3 KO clones 1 and 5 were purchased from Horizon Discovery (cat# HZGHC007500c001, and HZGHC007500c005) alongside Wild Type controls (cat# C631_29281, batch 40661 ~ Clone #1, and cat# C631_29281, batch 50047 ~ Clone #7)

value: KBM-7 (CML)-derived near-haploid cell line

value: MATR3 knockout


title: WT1,HAEED,DoxycyclineAddition, H3K27me3, Rep1


title: CPEP Uninfected, biological replicate 2

source_name: Primary human choroid plexus epithelial cell line, uninfected

value: untreated


title: CPEP JCPyV infected, biological replicate 1


title: H128 cells, siERRG2


title: CPEP JCPyV infected, biological replicate 3


title: 978-CNTNAP2-WT-AD-M_S6_L001

description:
978-CNTNAP2
S6

value: cerebella

value: WT

value: adult (AD)

value: WT-AD-M


title: BA-1

value: biliary atresia


title: MATR3 KO #1 rep1


title: CPEP Uninfected, biological replicate 3


title: WT1,EEDKO,DoxycyclineRemoval, H3K27me3, Rep1

value: Human embryonic kidney


title: CPEP Uninfected, biological replicate 1


title: MATR3 KO #5 rep2


title: WT1,EEDKO,DoxycyclineRemoval, H3K27me3, Rep2


title: H128 cells, siCont


title: WT1,EEDKO,DoxycyclineAddition, H3K27me3, Rep2


title: 607-CNTNAP2-KO-AD-F_S12_L001

description:
607-CNTNAP2
S12

value: KO

value: F

value: KO-AD-F


title: HAP1 WT #7 rep2

value: Wild Type


title: HAP1 WT #7 rep1


title: 333-CNTNAP2-KO-AD-M_S19_L001

description:
333-CNTNAP2
S19

value: M

value: KO-AD-M


title: 966-CNTNAP2-WT-P30-M_S21_L001

description:
966-CNTNAP2
S21

value: Thirty (30) days post-natal (P30)


title: FourWT0m [WT - 1]

value: wild type


title: 545-CNTNAP2-WT-P30-M_S24_L001

description:
545-CNTNAP2
S24


title: 891-CNTNAP2-KO-P30-F_S35_L001

description:
891-CNTNAP2
S35


title: CFPAC1 cells, control, resistant to SCH772984 (1uM), biological replicate 1

city: Durham

first: Daniel

middle: Philip

last: Nussbaum

state: NC

address: 203 Research Drive, MSRB1, Room 488

institute: Duke University

data_processing:
RNA-seq data was processed using the TrimGalore toolkit which employs Cutadapt to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads. Only reads that were 20nt or longer after trimming were kept for further analysis. Reads were mapped to the GRCh37v75 version of the human genome and transcriptome using the STAR RNA-seq alignment tool. Reads were kept for subsequent analysis if they mapped to a single genomic location.  Gene counts were compiled using the HTSeq tool. Only genes that had at least 10 reads in any given library were used in subsequent analysis. Normalization and differential expression was carried out using the DESeq2 Bioconductor package with the R statistical programming environment. The false discovery rate was calculated to control for multiple hypothesis testing. Gene set enrichment analysis was performed to identify gene ontology terms and pathways associated with altered gene expression for each of the comparisons performed
Supplementary files format and content: Single excel sheet

source_name: Cell line

growth_protocol: As described above

extract_protocol: RNeasy Kit (Qiagen)

treatment_protocol: As described above

value: Cell line

value: Pancreatic ductal adenomcarcinoma

value: KRAS-mutant

value: SCH772984 (1uM) x8weeks


title: TFRC,DoxycyclineRemoval, H3K27me3, Rep1


title: CFPAC1 cells, control, resistant to SCH772984 (1uM), biological replicate 3


title: CFPAC1 cells, control, resistant to SCH772984 (1uM), biological replicate 2


title: WT1,EEDKO,DoxycyclineAddition, H3K27me3, Rep1


title: HAP1 WT #1 rep2

value: KBM-7 (CML)-derived near-haploid cell line


title: MATR3 KO #1 rep2

value: MATR3 knockout


title: HAP1 WT #1 rep3


title: CFPAC1 cells, control, treated with SCH772984 (1uM) for one week, biological replicate 3

value: SCH772984 (1uM) x1week


title: 795-CNTNAP2-WT-AD-F_S1_L001

description:
795-CNTNAP2
S1

value: cerebella

value: WT

value: adult (AD)

value: WT-AD-F


title: 836-CNTNAP2-WT-AD-F_S5_L001

description:
836-CNTNAP2
S5

value: F


title: CFPAC1 cells, control, treated with SCH772984 (1uM) for one week, biological replicate 2


title: TFRC, NoDoxycycline, H3K27me3, Rep1

value: Human embryonic kidney


title: 985-CNTNAP2-WT-AD-F_S3_L001

description:
985-CNTNAP2
S3


title: iPSC-NPC-Organoid-PCTME

city: Chicago

first: Xiao

last: Song

state: IL

address: 303 E Superior St, Lurie 6-250

department: Neurology

institute: Northwestern University Feinberg School of Medicine

data_processing:
Reads were aligned to the human genome hg19 using HISAT2, version 2.1.0.
For xenograft samples, the Disambiguate tool (AstraZeneca-NGS) was used to separate sequence reads originating from human iPSC cells and mouse stomal component after alignment. The reads assigned to human species were used for gene expression and alternative splicling analysis.
Quantification was performed using HTSeq-count, version 0.13.5.
The counts for a gene in each sample was normalized by DESeq2, version 1.34.0.
The mapped reads were processed through the MISO (version 0.5.4) pipeline to estimate expression of alternatively spliced isoforms.
Assembly: hg19
Supplementary files format and content: HTSeq-count files include raw counts for each gene of each sample generated from HTSeq-count.
Supplementary files format and content: MISO files include Percent Spliced In (PSI) values for each AS events of each sample generated from MISO-run and MISO-summary.
Supplementary files format and content: Normalized_counts files include the normalized counts for each gene in all samples generated from DESeq2.

molecule: polyA RNA

growth_protocol: iPSC-NPCs were cultured in N2B27 medium (50% DMEM/F12 and 50% Neurobasal-A medium supplemented with GlutaMAX, 1 × N-2 supplement, 1 × B-27 supplement, 1 × antibiotic-antimycotic, 150 µM ascorbic acid) plus 3 μM CHIR99021 and 1 μM SAG. Organoids were cultured in N2B27 medium plus 10% FBS.

extract_protocol:
RNA was isolated using the Qiagen RNeasy Mini kit according to the manufacturer's instruction. 1 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module, Ultra II RNA Library Prep Kit, and Multiplex Oligos (NEB, Cat #E7490, E7775, E6609) according to the manufacturer's instruction.

treatment_protocol: For organoid samples, edited NPCs were cultured in 3D organoid with N2B27+10%FBS medium for 14 days. For xenograft samples, NPCs with different genotypes were intracranially transplanted into athymic mice. Mice were sacrificed when pathologic symptoms developed resulting from tumor burden or 120 days post brain transplantation. RNAs were extracted from the tumor region of brain tissue sections and subjected to RNA-seq analysis.

value: Edited human iPSC12-derived NPCs

value: PTEN-/-, CDKN2A/B-/-, TERTp-C228T/WT, MTAP-/-, EGFRvIII

value: cultured in 3D organoid


title: CFPAC1 cells, control, treated with SCH772984 (1uM) for one week, biological replicate 1


title: 606-CNTNAP2-WT-AD-F_S4_L001

description:
606-CNTNAP2
S4


title: iPSC-NPC-Organoid-PCTE

value: PTEN-/-, CDKN2A/B-/-, TERTp-C228T/WT, EGFRvIII


title: CFPAC1 cells, control, treated with DMSO (1:1,000) for one week, biological replicate 3

value: Cell line

value: Control (DMSO, 1:1,000) x1 week


title: TFRC,DoxycyclineAddition, H3K27me3, Rep1


title: CFPAC1 cells, control, treated with DMSO (1:1,000) for one week, biological replicate 1

value: Pancreatic ductal adenomcarcinoma

value: KRAS-mutant


title: WT1,DoxycyclineAddition, H3K27me3, Rep1


title: WT1,DoxycyclineRemoval, H3K27me3, Rep1


title: WT1,DoxycyclineAddition, H3K27me3, Rep2


title: iPSC-NPC-Organoid-PCT

value: PTEN-/-, CDKN2A/B-/-, TERTp-C228T/WT


title: 822-CNTNAP2-KO-AD-M_S18_L001

description:
822-CNTNAP2
S18

value: KO

value: M

value: KO-AD-M


title: CFPAC1 cells, control, treated with DMSO (1:1,000) for one week, biological replicate 2


title: iPSC-NPC-Organoid-PCTM

value: PTEN-/-, CDKN2A/B-/-, TERTp-C228T/WT, MTAP-/-


title: 561-CNTNAP2-WT-P30-F_S28_L001

description:
561-CNTNAP2
S28

value: cerebella

value: WT

value: Thirty (30) days post-natal (P30)


title: 543-CNTNAP2-WT-P30-F_S27_L001

description:
543-CNTNAP2
S27

value: F


title: iPSC-NPC-Organoid-TIA

value: Edited human iPSC12-derived NPCs


title: 927-CNTNAP2-KO-P30-F_S37_L001

description:
927-CNTNAP2
S37


title: iPSC-NPC-Organoid-TI


title: 107-CNTNAP2-WT-AD-M_S9_L001

description:
107-CNTNAP2
S9

value: adult (AD)

value: WT-AD-M


title: WT1, NoDoxycycline, H3K27me3, Rep1

value: Human embryonic kidney


title: SW620 cells, control, treated with SCH772984 (1uM) and Senexin A (1uM)  for one week, biological replicate 2

value: Cell line

value: Colorectal adenocarcinoma

value: SCH772984 (1uM) + Senexin A (1uM) x8weeks


title: SW620 cells, control, treated with SCH772984 (1uM) and Senexin A (1uM) for one week, biological replicate 3

value: KRAS-mutant


title: WT1,DoxycyclineRemoval, H3K27me3, Rep2


title: HAP1 WT #1 rep1

value: KBM-7 (CML)-derived near-haploid cell line

value: Wild Type


title: SW620 cells, control, treated with SCH772984 (1uM) and Senexin A (1uM) for one week, biological replicate 1


title: iPSC-NPC-Organoid-TA

value: cultured in 3D organoid


title: 3152PBLs-PSPB6

city: University Park

first: Troy

middle: L

last: Ott

state: PA

address: 107 AVBS Building

department: Animal Science

institute: Penn State University

data_processing:
Transcriptome data were processed according to BGI bioinformatic pipeline. Raw reads were filtered using SOAPnuke v1.5.2 software (Cock et al., 2010) and samples averaged 92% clean reads. Clean reads were aligned to the reference genome GCF_000003205.7_Btau_5.0.1 (Bos taurus, NCBI) using HISAT2 v2.0.4 software (Kim et al., 2015) for identification of novel transcripts with an average alignment ratio of 90%. Clean reads were mapped to the annotated transcriptome using Bowtie2 v2.2.5 software (Langmead & Salzberg, 2012) with an average alignment ratio of 70%. A total of 18,801 genes were detected. Then, gene expression of each sample was calculated from reads mapped to the transcriptome using RSEM v1.2.8 software (Li & Dewey, 2011), and the DEseq2 method (Love et al., 2014) was used for detection of differentially expressed genes (DEG) in the comparison PSPB6 versus IFNT6.
Assembly: GCF_000003205.7_Btau_5.0.1
Supplementary files format and content: Excel (.xlsx), results of gene expression calculated from individual read counts using RSEM v1.2.8 software and the DEseq2 method.
Supplementary files format and content: NCBI Gene ID, Ensembl Gene ID, Other Symbols, GeneBank Desc, Gene Symbol, log2, Qvalue, Pvalue, Transcripts number, Transcripts ID, TPM, Read Count, FPKM

organism: Bos taurus

source_name: Peripheral blood leukocytes

growth_protocol: Postpubertal Holstein heifers (virgin; 12-17 months of age) were estrous synchronized with an intramuscular injection of a PGF2A analog (Estroplan, 500 μg of cloprostenol sodium, Parnell) and were monitored for estrus behavior (day 0). Thirteen days after the onset of estrus, heifers were moved to tie- stall pens where they remained for 4 or 7 days. Animals were housed in pairs and fed a typical heifer total mixed ration once daily. In the morning of day 14, animals received caudal epidural anesthesia using lidocaine (5-8 mL of 2% lidocaine hydrochloride, Aspen Veterinary Resources). Then, a 16 Fr silicone Foley catheter (Bardex) was inserted through the cervix and a sterilized tubing connector with custom made cap were placed into the drainage channel to seal catheter from environmental contamination.

extract_protocol:
Blood was collected at the end of the treatment schedule, 12 hours after last infusion (8:30 am of day 17 or day 20). Blood was collected from tail vein into K3 EDTA vacuette tubes (Greiner Bio- one) and peripheral blood leukocytes (PBLs) were isolated as described in Kamat et al., (2016). RNA was isolated from PBLs isolate (15 million cells) following homogenization in 800 μL of TRIzol reagent (Life Technologies). Total RNA was purified using RNA Clean and Concentrator kit (Zymo Research) to eliminate contaminating DNA and reagents. RNA samples were shipped on dry ice to BGI laboratory (Beijing Genomics Institute, Shenzhen, China) where RNA quality and quantity were assessed using Agilent 2100 Bioanalyzer (Agilent Technologies). All samples met the quality criteria for RNA sequencing, showing RNA integrity number (RIN) between 8 and 9.9 values.
Preparation of mRNA library and sequencing were performed following BGI DNBSEQ technology platform with paired end 100 bp (PE100).

treatment_protocol: Vehicle solution was prepared with 200 μg/mL bovine serum albumin (BSA) fraction V (OmniPur) in PBS, sterilized using a vacuum filtration system with polyethersulfone (PES) membrane (2 μm pore size; 53 VWR), and stored at 4°C. Each treatment infusion had a total volume of 20 mL and consisted of either vehicle + 200 μg of IFNT (10 μg/mL), or vehicle + 200 μg of IFNT + 100 μg of PAG (5 μg/mL). Treatments were prepared using recombinant ovine IFNT (kindly supplied by Fuller Bazer, Texas A&M University) and PAG purified from first-trimester bovine placenta (kindly supplied by Josh Branen, Biotracking LLC Inc). Heifers (N = 4 per treatment) were randomly assigned to one of the following treatment schedules: vehicle + IFNT from day 14 to 19 (IFNT6), and vehicle + IFNT from day 14 to 16 followed by vehicle + IFNT + PAG from day 17 to 19 (PSPB6).

value: Peripheral blood leukocytes

tag: breed

value: Holstein heifers

value: 12-17 months

value: IFNT+PAG


title: 925-CNTNAP2-KO-P30-F_S39_L001

description:
925-CNTNAP2
S39

value: cerebella

value: KO

value: Thirty (30) days post-natal (P30)


title: 3151PBLs-PSPB6


title: WT1, NoDoxycycline, H3K27me3, Rep2


title: SW620 cells, control, resistant to SCH772984 (1uM), biological replicate 2

value: SCH772984 (1uM) x8weeks


title: Plasma miRNA-seq at ET11 of NP  YFC-98 [YFC-98-2]

last: Zeng

state: Hunan

address: 87 Xiangya Street

department: Reproductive medicine center

institute: Xiangya Hospital Central South University

data_processing:
MicroRNA-seq was performed with the Illumina NovaSeq 6000 (Illumina, USA) following the manufacturer’s instructions. After sequencing, the adaptor sequences were trimmed and the quality-filtered reads were harvested as clean reads using fastx (version 0.0.13). The clean reads were mapped to databases of the human genome, RFam, RepBase, mRNA database, and miRBase using the bowtie software, allowing up to one mismatch. Based on the miRNA biogenesis model, we used the miRCat software to predict novel miRNAs. Then, the clean reads of each sample were aligned to merged miRNA databases (known miRNAs from miRBase plus the newly predicted miRNAs) to calculate the miRNA expression levels. The numbers of mapped tags were defined as the raw expression levels of the miRNAs. T.e counts were normalized by TPM method.
Assembly: GRCh38
Supplementary files format and content: TPM_all_samples.csv: csv file includes TPM nomalized values for each sample.

extract_protocol:
The miRNAs were extracted from the plasma using the mirVana™ miRNA Isolation Kit (Cat #. AM1561, Austin TX, USA) according to the manufacturer’s protocol. The concentration and quality of RNA samples were determined by NanoDrop ND-1000 spectrophotometer (Thermo Fisher, Wilmington, DE, USA) and 2100 Bioanalyzer Instruments (Agilent Technologies, Santa Clara, CA, USA).
The miRNA sequencing library was constructed using the QIAseq miRNA Library Kit (QIAGEN, German). The total RNA of each sample was used to prepare the miRNA sequencing library as the following steps: 3'-adaptor ligation, 5'-adaptor ligation, cDNA synthesis, PCR amplification, and gel purification. After quantification with Qubit (Thermo Fisher, USA), the libraries were captured on cBOT (Illumina, USA) to be amplified in situ as clusters following cBot User Guide.

value: blood

tag: sample type

value: plasma

tag: bmi

tag: endometrial thickness_at_et

tag: number of_transferred_embryos

tag: stage of_transferred_embryos

value: blastocyst

tag: timing of_sample_collection

tag: reproductive outcome

value: NP


title: 3121PBLs-PSPB6

tag: tissue

tag: treatment


title: SW620 cells, control, resistant to SCH772984 (1uM), biological replicate 3

value: Cell line

value: Colorectal adenocarcinoma

tag: genotype


title: 926-CNTNAP2-KO-P30-F_S36_L001

description:
926-CNTNAP2
S36

tag: age

tag: Sex

value: F


title: 3070PBLs-PSPB6


title: Plasma miRNA-seq at ET11 of NP  YFC-85 [YFC-85-2]

value: morula


title: SW620 cells, control, resistant to SCH772984 (1uM), biological replicate 1

tag: cell line

value: KRAS-mutant


title: Plasma miRNA-seq at ET11 of NP  YFC-71 [YFC-71-2]


title: SW620 cells, control, treated with SCH772984 (1uM) for one week, biological replicate 3

tag: cell type

value: SCH772984 (1uM) x1week


title: 3155PBLs-IFNT6

value: Peripheral blood leukocytes

value: Holstein heifers


title: 3148PBLs-IFNT6

value: 12-17 months


title: Plasma miRNA-seq at ET11 of NP  YFC-84 [YFC-84-2]


title: 531-CNTNAP2-WT-P30-M_S20_L001

description:
531-CNTNAP2
S20

value: cerebella

value: WT

value: M

tag: groups


title: SW620 cells, control, treated with SCH772984 (1uM) for one week, biological replicate 2


title: Plasma miRNA-seq at ET11 of NP  YFC-140 [YFC-140-2]


title: 808-CNTNAP2-KO-AD-F_S11_L001

description:
808-CNTNAP2
S11

value: KO

value: adult (AD)

value: KO-AD-F


title: 3125PBLs-IFNT6


title: SW620 cells, control, treated with SCH772984 (1uM) for one week, biological replicate 1


title: 930-CNTNAP2-KO-P30-M_S32_L001

description:
930-CNTNAP2
S32

value: Thirty (30) days post-natal (P30)


title: iPSC-NPC-Organoid-T

value: Edited human iPSC12-derived NPCs

value: cultured in 3D organoid


title: Plasma miRNA-seq at ET11 of NP  YFC-92 [YFC-92-2]

value: blood

value: plasma

value: NP


title: 3123PBLs-IFNT6


title: SW620 cells, control, treated with DMSO (1:1,000) for one week, biological replicate 3

value: Cell line

value: Colorectal adenocarcinoma

value: KRAS-mutant

value: Control (DMSO, 1:1,000) x1 week


title: 924-CNTNAP2-WT-P30-F_S26_L001

description:
924-CNTNAP2
S26

value: F


title: Plasma miRNA-seq at ET11 of NP  YFC-87 [YFC-87-2]

value: blastocyst


title: 3152Endo-PSPB6

data_processing:
Transcriptome data were processed according to BGI bioinformatic pipeline. Raw reads were filtered using SOAPnuke v1.5.2 software (Cock et al., 2010) and samples averaged 92% clean reads. Clean reads were aligned to the reference genome GCF_000003205.7_Btau_5.0.1 (Bos taurus, NCBI) using HISAT2 v2.0.4 software (Kim et al., 2015) for identification of novel transcripts with an average alignment ratio of 90%. Clean reads were mapped to the annotated transcriptome using Bowtie2 v2.2.5 software (Langmead & Salzberg, 2012) with an average alignment ratio of 70%. A total of 18,801 genes were detected. Then, gene expression of each sample was calculated from reads mapped to the transcriptome using RSEM v1.2.8 software (Li & Dewey, 2011), and the DEseq2 method (Love et al., 2014) was used for detection of differentially expressed genes (DEG) in the following comparison groups: (1) IFNT3 versus BSA3, (2) IFNT6 versus IFNT3, and (3) PSPB6 versus IFNT6.
Assembly: GCF_000003205.7_Btau_5.0.1
Supplementary files format and content: Excel (.xlsx), results of gene expression calculated from individual read counts using RSEM v1.2.8 software and the DEseq2 method.
Supplementary files format and content: NCBI Gene ID, Ensembl Gene ID, Other Symbols, GeneBank Desc, Gene Symbol, log2, Qvalue, Pvalue, Transcripts number, Transcripts ID, TPM, Read Count, FPKM

source_name: Endometrium

extract_protocol:
Tissue samples were collected at the end of the treatment schedule, 12 hours after last infusion (8:30 am of day 17 or day 20). Animals received caudal epidural anesthesia and a sterilized custom-made mini-Tischler biopsy forceps with a 22 inch shaft length, 4 mm shaft diameter, and 4x8 mm bite size (Aries surgical, Davis CA) was passed through the cervix for collection of 1 endometrial biopsy. The biopsies were immediately placed into sterilized cryotubes and snap-frozen in liquid nitrogen. RNA was isolated from one frozen endometrial biopsy (~50-60 mg) following homogenization in 800 μL of TRIzol reagent (Life Technologies). Total RNA was purified using RNA Clean and Concentrator kit (Zymo Research) to eliminate contaminating DNA and reagents. Endometrial RNA samples were shipped on dry ice to BGI laboratory (Beijing Genomics Institute, Shenzhen, China) where RNA quality and quantity were assessed using Agilent 2100 Bioanalyzer (Agilent Technologies). All samples met the quality criteria for RNA sequencing, showing RNA integrity number (RIN) between 8 and 9.9 values.
Preparation of mRNA library and sequencing were performed following BGI DNBSEQ technology platform with paired end 100 bp (PE100).

treatment_protocol: Vehicle solution was prepared with 200 μg/mL bovine serum albumin (BSA) fraction V (OmniPur) in PBS, sterilized using a vacuum filtration system with polyethersulfone (PES) membrane (2 μm pore size; 53 VWR), and stored at 4°C. Each treatment infusion had a total volume of 20 mL and consisted of either vehicle only, vehicle + 200 μg of IFNT (10 μg/mL), or vehicle + 200 μg of IFNT + 100 μg of PAG (5 μg/mL). Treatments were prepared using recombinant ovine IFNT (kindly supplied by Fuller Bazer, Texas A&M University) and PAG purified from first-trimester bovine placenta (kindly supplied by Josh Branen, Biotracking LLC Inc). Heifers (N = 4 per treatment) were randomly assigned to one of the following treatment schedules: vehicle from day 14 to 16 of the estrous cycle (BSA3), vehicle + IFNT from day 14 to 16 (IFNT3), vehicle + IFNT from day 14 to 19 (IFNT6), and vehicle + IFNT from day 14 to 16 followed by vehicle + IFNT + PAG from day 17 to 19 (PSPB6).

value: Endometrium

value: Holstein heifers

value: 12-17 months

value: IFNT+PAG


title: 928-CNTNAP2-KO-P30-M_S31_L001

description:
928-CNTNAP2
S31

value: cerebella

value: KO

value: M


title: SW620 cells, control, treated with DMSO (1:1,000) for one week, biological replicate 2


title: 824-CNTNAP2-KO-AD-F_S14_L001

description:
824-CNTNAP2
S14

value: adult (AD)

value: KO-AD-F


title: SW620 cells, control, treated with DMSO (1:1,000) for one week, biological replicate 1


title: 3121Endo-PSPB6


title: Plasma miRNA-seq at ET11 of NP  YFC-101 [YFC-101-2]

value: blood

value: plasma

value: morula


title: 3151Endo-PSPB6


title: Plasma miRNA-seq at ET11 of NP  YFC-56 [YFC-56-2]

value: NP


title: 108-CNTNAP2-KO-AD-M_S16_L001

description:
108-CNTNAP2
S16

value: KO-AD-M


title: SW1573 cells, control, treated with SCH772984 (1uM) and Senexin A (1uM) for one week, biological replicate 3

value: Cell line

value: Lung adenocarcinoma

value: KRAS-mutant

value: SCH772984 (1uM) + Senexin A (1uM) x8weeks


title: Plasma miRNA-seq at ET11 of NP YFC-1 [YFC-1-2]

value: blastocyst


title: 968-CNTNAP2-KO-P30-M_S33_L001

description:
968-CNTNAP2
S33

value: Thirty (30) days post-natal (P30)


title: 702-CNTNAP2-KO-AD-F_S13_L001

description:
702-CNTNAP2
S13

value: F


title: SW1573 cells, control, treated with SCH772984 (1uM) and Senexin A (1uM) for one week, biological replicate 1


title: 3070Endo-PSPB6

value: Endometrium

value: Holstein heifers

value: 12-17 months

value: IFNT+PAG


title: Plasma miRNA-seq at ET0 of NP  YFC-98 [YFC-98-1]


title: SW1573 cells, control, treated with SCH772984 (1uM) and Senexin A (1uM)  for one week, biological replicate 2


title: 3148Endo-IFNT6


title: 3155Endo-IFNT6


title: 825-CNTNAP2-KO-AD-F_S15_L001

description:
825-CNTNAP2
S15

value: cerebella

value: KO

value: adult (AD)

value: KO-AD-F


title: Plasma miRNA-seq at ET0 of NP  YFC-71 [YFC-71-1]

value: blood

value: plasma

value: morula

value: NP


title: 46-CNTNAP2-WT-AD-M_S7_L001

description:
46-CNTNAP2
S7

value: WT

value: M

value: WT-AD-M


title: SW1573 cells, control, resistant to SCH772984 (1uM), biological replicate 2

value: Cell line

value: Lung adenocarcinoma

value: KRAS-mutant

value: SCH772984 (1uM) x8weeks


title: Plasma miRNA-seq at ET0 of NP  YFC-85 [YFC-85-1]


title: SW1573 cells, control, resistant to SCH772984 (1uM), biological replicate 3


title: 565-CNTNAP2-WT-P30-F_S29_L001

description:
565-CNTNAP2
S29

value: Thirty (30) days post-natal (P30)

value: F


title: Plasma miRNA-seq at ET0 of NP  YFC-84 [YFC-84-1]


title: 3123Endo-IFNT6

value: Endometrium

value: Holstein heifers

value: 12-17 months


title: 429-CNTNAP2-KO-P30-M_S34_L001

description:
429-CNTNAP2
S34

value: cerebella

value: KO


title: SW1573 cells, control, resistant to SCH772984 (1uM), biological replicate 1


title: 797-CNTNAP2-WT-AD-F_S2_L001

description:
797-CNTNAP2
S2

value: adult (AD)

value: WT-AD-F


title: 3158Endo-IFNT3


title: 537-CNTNAP2-WT-P30-F_S25_L001

description:
537-CNTNAP2
S25


title: 3145Endo-IFNT3


title: Plasma miRNA-seq at ET0 of NP  YFC-92 [YFC-92-1]

value: blood

value: plasma

value: morula

value: NP


title: Wt, Total, Rep2, Paf1CD

city: Pittsburgh

first: Karen

last: Arndt

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
Alignments were then converted to bam and duplicates were marked and removed using the samtools suite
Ribosomal RNA loci were blacklisted for subsequent analysis using bedtools intersect
Reads mapping to S. pombe were separated from those mapping to S. cerevisiae by selecting chromosomes to retain with samtools view
S. pombe reads over coding features were counted with Rsubread featureCounts
DESeq2 estimateSizeFactors() function used to generate normalization factors.
Bam files were converted to strand-specific bigWig format using deepTools2 bamCoverage using DESeq2-derived spike-in size factors.
Assembly: S. cerevisiae: Ensembl R64-3-1/S.pombe: ASM294v2 Hybrid Genome
Supplementary files format and content: bigwig file of spike-in normalized reads mapping to forward strand
Supplementary files format and content: bigwig file of spike-in normalized reads mapping to reverse strand

organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

source_name: MATa his4-912δ lys2-128δ leu2Δ1 trp1Δ63

growth_protocol: S. cerevisiae and S. pombe were grown in YPD standard rich growth medium supplemented with 400 μM tryptophan at 30°C.

extract_protocol:
4tU-labeled S.cerevisiae pellets were spiked-in with labeled S. pombe at a 14:1 OD600 ratio and total RNA extracted with a hot acid-phenol extraction.
4tU-seq libraires were prepared using the TECAN Ovation SoLo RNA-seq library preparation kit (TECAN, Redwood City, CA; 0516–32) targeting S. cerevisiae rRNAs for depletion using AnyDeplete technology. 2-10 ng of RNA was used per library build and fragment distributions assesed by tapestation

treatment_protocol: Once S. cerevisiae  OD600 = 1.0-1.2 was reached, 4tU was added to 30 OD600 of culture to a final concentration of 0.65 mg/mL for precisely 5 min at RT before quenching by pouring cultures into 1/2 volume of dry-ice-cold methanol. Cells were pelleted and snap frozen before sonication.


title: Plasma miRNA-seq at ET0 of NP  YFC-87 [YFC-87-1]

value: blastocyst


title: SW1573 cells, control, treated with SCH772984 (1uM) for one week, biological replicate 2

value: Cell line

value: Lung adenocarcinoma

value: SCH772984 (1uM) x1week


title: 3125Endo-IFNT6


title: SW1573 cells, control, treated with SCH772984 (1uM) for one week, biological replicate 1

value: KRAS-mutant


title: 3106Endo-IFNT3


title: 3134Endo-IFNT3


title: rtf1D, Total, Rep2, Paf1CD

source_name: MATα his4-912δ lys2-128δ leu2Δ1 trp1Δ63 rtf1Δ::KANMX


title: 3168Endo-BSA3


title: SW1573 cells, control, treated with DMSO (1:1,000) for one week, biological replicate 2

value: Control (DMSO, 1:1,000) x1 week


title: Wt, Total, Rep1, Paf1CD


title: rtf1D, Total, Rep1, Paf1CD


title: Plasma miRNA-seq at ET0 of NP  YFC-56 [YFC-56-1]


title: SW1573 cells, control, treated with DMSO (1:1,000) for one week, biological replicate 3


title: Plasma miRNA-seq at ET14 of CP YFC-90 [YFC-90-3]

value: cleavage

value: CP


title: paf1D, Total, Rep2, Paf1CD

source_name: MATα his4-912δ lys2-128δ leu2Δ1 trp1Δ63 paf1Δ::KANMX


title: 3120Endo-BSA3

value: Endometrium

value: Holstein heifers

value: 12-17 months


title: MIA PaCa-2 cells, control, resistant to SCH772984 (1uM), biological replicate 3

value: MIA PaCa-2

value: Pancreatic ductal adenomcarcinoma

value: SCH772984 (1uM) x8weeks


title: SW1573 cells, control, treated with DMSO (1:1,000) for one week, biological replicate 1


title: SW1573 cells, control, treated with SCH772984 (1uM) for one week, biological replicate 3


title: Plasma miRNA-seq at ET0 of NP  YFC-140 [YFC-140-1]

value: blood

value: plasma


title: Plasma miRNA-seq at ET14 of CP YFC-135 [YFC-135-3]

value: morula


title: 3046Endo-BSA3


title: Plasma miRNA-seq at ET14 of CP YFC-116 [YFC-116-3]

value: blastocyst


title: leo1D, Total, Rep2, Paf1CD

source_name: MATa his4-912δ lys2-128δ ura3-52 trp1Δ63 leo1Δ::KanMX


title: Plasma miRNA-seq at ET0 of NP  YFC-101 [YFC-101-1]

value: NP


title: MIA PaCa-2 cells, control, resistant to SCH772984 (1uM), biological replicate 1

value: Cell line


title: MLL-AF9;Traf6-/-_3

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Adaptor sequences were trimmed from the raw RNA-seq reads with fastp (v 0.23.1). Trimmed reads of each sample were mapped to the reference human genome hg38 and mouse genome mm10 by using STAR (v 2.3.1) and normalized to 1 million reads in the original library.
The quality of paired reads were checked using FASTQC (v0.11.7)
Reads were aligned against human mm10 genome using HISAT2 (v2.0.5)
Each gene-level raw counts were calculated using featureCounts (v1.5.2)
Assembly: hg38 and mm10
Supplementary files format and content: The CSV file include raw read counts for each sample

source_name: hematopoietic cells

growth_protocol: The cells were cultured in RPMI1640 medium with 10% fetal bovine serum FBS and 1% penicillin and streptomycin . 10ng/mL of human IL-3 was added to the medium for culturing TF-1. MLL-AF9-expressing cells were cultured with IMDM) with 10% FCS, 10 ng/mL of SCF, 10 ng/mL of IL-3, and 10 ng/mL of IL-6.

extract_protocol:
RNA was extracted using RNeasy Plus Mini Kit (Qiagen) following manufacturer's protocol
RNA libraries were prepared according to the protocol of QuantSeq 3'mRNA-Seq Library Prep Kit FWD (Lexogen).

treatment_protocol: To induce knockdown of TRAF6 in human cells, the cells were cultured with doxycycline (1μg/mL) for 7 days. For knockout of Traf6 in murine AML cells, the leukemic cells were cultured with 1μM 4-hydroxytamoxifen for 4 days.

value: hematopoietic cells

value: leukemic cells

value: Traf6 knockout


title: MLL-AF9;Traf6-/-_2


title: leo1D, Total, Rep1, Paf1CD


title: Plasma miRNA-seq at ET14 of CP YFC-55 [YFC-55-3]


title: Plasma miRNA-seq at ET0 of NP YFC-1 [YFC-1-1]


title: 3073Endo-BSA3


title: MIA PaCa-2 cells, control, treated with SCH772984 (1uM) for one week, biological replicate 3

value: KRAS-mutant

value: SCH772984 (1uM) x1week


title: Plasma miRNA-seq at ET14 of CP YFC-78 [YFC-78-3]

value: CP


title: MLL-AF9;Traf6-/-_1


title: ctr9D, Total, Rep1, Paf1CD

source_name: MATα his4-912δ lys2-128δ trp1Δ63 ctr9Δ::KANMX


title: MIA PaCa-2 cells, control, treated with SCH772984 (1uM) for one week, biological replicate 2


title: ctr9D, Total, Rep2, Paf1CD


title: paf1D, Total, Rep1, Paf1CD


title: MLL-AF9;Traf6+/+_3

value: WT


title: Plasma miRNA-seq at ET14 of CP YFC-70 [YFC-70-3]


title: Plasma miRNA-seq at ET14 of CP YFC-109 [YFC-109-3]


title: cdc73D, Total, Rep2, Paf1CD

source_name: MATa his4-912δ lys2-128δ trp1Δ63 cdc73Δ::KANMX


title: MIA PaCa-2 cells, control, treated with SCH772984 (1uM) for one week, biological replicate 1


title: MLL-AF9;Traf6+/+_2


title: MLL-AF9;Traf6+/+_1


title: MIA PaCa-2 cells, control, treated with DMSO (1:1,000) for one week, biological replicate 2

value: Control (DMSO, 1:1,000) x1 week


title: Plasma miRNA-seq at ET14 of CP YFC-74 [YFC-74-3]

value: cleavage


title: MIA PaCa-2 cells, control, resistant to SCH772984 (1uM), biological replicate 2

value: MIA PaCa-2

value: Pancreatic ductal adenomcarcinoma


title: MIA PaCa-2 cells, control, treated with DMSO (1:1,000) for one week, biological replicate 3


title: cdc73D, Total, Rep1, Paf1CD


title: Plasma miRNA-seq at ET14 of CP YFC-64 [YFC-64-3]

value: blood


title: Wt, H3K364tU, Rep2, H3K36

description: 4tU-labled RNA

library_source: other

data_processing:
Alignments were then converted to bam and duplicates were marked and removed using the samtools suite
S. cerevisiae Ribosomal RNA loci were blacklisted for subsequent analysis using bedtools intersect
Reads mapping to S. pombe were separated from those mapping to S. cerevisiae by selecting chromosomes to retain with samtools view
S. pombe reads over coding features were counted with Rsubread featureCounts
DESeq2 estimateSizeFactors() function used to generate normalization factors.
Bam files were converted to strand-specific bigWig format using deepTools2 bamCoverage using DESeq2-derived spike-in size factors.
Assembly: S. cerevisiae: Ensembl R64-3-1/S.pombe: ASM294v2 Hybrid Genome
Supplementary files format and content: bigwig file of spike-in normalized reads mapping to forward strand
Supplementary files format and content: bigwig file of spike-in normalized reads mapping to reverse strand
Library strategy: 4tU-seq

molecule: other

source_name: MATα his3Δ200 ura3-52

extract_protocol:
4tU-labeled S.cerevisiae pellets were spiked-in with labeled S. pombe at a 14:1 OD600 ratio and total RNA extracted with a hot acid-phenol extraction. 4tU-RNA labled was biotinylated with MTSEA-XX biotin and pulled down using Dynabeads MyOne Streptavidin C1 beads. RNA was purified using the RNEasy kit and quantified by Qubit.
4tU-seq libraires were prepared using the TECAN Ovation SoLo RNA-seq library preparation kit (TECAN, Redwood City, CA; 0516–32) targeting S. cerevisiae rRNAs for depletion using AnyDeplete technology. 2-10 ng of RNA was used per library build and fragment distributions assesed by tapestation

tag: time (minutes)


title: MIA PaCa-2 cells, control, treated with DMSO (1:1,000) for one week, biological replicate 1


title: iTreg_72h_LIRIL2R_LNA2_rep4

data_processing:
There were 10-25 million reads per sample with a median at around 15 million reads. The data were pseudo-aligned with kallisto (64). For kallisto run, the transcriptome file was downloaded from UCSC table browser using following description: Clad: mammal; Genome: human; Assembly: hg38; Group: genes and gene predictions; Track ncbi refseq; Table ucsc refseq (refgene); Region genome; Output format sequence; Output file hg38_refseq.
The data were single ended. Therefore, one has to provide the fragment length parameter for kallisto run. From the library, the length was estimated to be 275 +/- 100. Differential expression analysis on kallisto-quantified count data between NT and LIRIL2R LNA-treated samples was performed using sleuth (65).
Assembly: hg38
Supplementary files format and content: a folder containing the output of kallisto pseudoalignment. The count table contains estimated TPM values in a tsv file.

source_name: blood

extract_protocol:
RNA was isolated (RNeasy Mini Kit, cat# 74106, QIAGEN) and treated in-column with DNase (RNase-Free DNase Set; QIAGEN) for 15 min. The removal of genomic DNA was ensured by an additional treatment of the samples with DNase I (Invitrogen). RNA quantification was performed using Nanodrop 2000 and quality control was performed using BioRad Experion or Agilent Bioanalyzer.
Libraries for RNA-Seq were prepared using Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part #15031047). The quality of the libraries was confirmed with Advanced Analytical Fragment Analyzer, and the concentrations of the libraries were quantified with Qubit® Fluorometric Quantitation (Life Technologies).
24h samples were sequenced togother in two lanes. Each sample was sequenced on both lanes. 48h and 72h samples were sequenced togther in one lane. Samples for 24h were prepared at different times as compared to 48h and 72h, which were prepared from the same culture. Sequencing was performed at the Finnish Functional Genomics Centre using the HiSeq3000 Next-Generation Sequencing platform.

value: CD4+ T cells

value: LIRIL2R LNA2

value: Activated under iTreg condition for 72 hours


title: E13 Submandibular gland epithelium

first: Rei

last: Sekiguchi

state: Maryland

address: 30 Convent Drive

department: CBS

institute: NIDCR

library_source: transcriptomic single cell

data_processing:
Reads were mapped using GRCm38-2020-A reference transcriptome
Sequencing data was processed using the 10X genomics Cell Ranger v2.1.1 pipeline
Secondary analysis was performed using Seurat v3 R package
Assembly: Reads were mapped using the mm10 reference transcriptome from 10X Genomics
Supplementary files format and content: Cellranger filtered feature barcode matrix in HDF5 format
Supplementary files format and content: Cellranger raw feature barcode matrix in HDF5 format

source_name: Submandibular gland

extract_protocol:
Submandibular and parotid glands at E13, approximately 10 of each, were harvested from mouse embryos in cold DMEM/F12 (Life Technologies). To separate the epithelium from the mesenchyme, salivary glands were treated with Dispase II (Thermo Fisher Scientific) at 37 ºC with 5% CO2 for 10 minutes. To dissociate these separated tissues into single cells, salivary epithelium and mesenchyme were separately digested in 1.5-ml tubes containing cold protease solution: 10 mg/ml Bacillus Licheniformis protease (Creative Enzymes NATE0633)(Adam et al. 2017), 40 μl Accutase, and 40 μl Accumax (Innovative Cell Technologies). The protease digestion was inhibited by the addition of 1 ml of cold DMEM/F12 with 10% fetal bovine serum (FBS) to the protease solution. The cells were filtered through a 40-μm strainer (Bel-Art Productions). The dissociated cells were pelleted in a swinging bucket centrifuge . The supernatant was aspirated until only 20-30 μl remained. After adding 1 ml of cold DMEM/F12 containing 1% FBS for a second wash, the cells were again pelleted. The supernatant was aspirated, and the cells were resuspended and placed on ice until single-cell capture. Cell viability and concentration were evaluated using acridine orange dye and a Cellometer Auto 2000 (Nexcelom Bioscience). Cell viability of >95% was observed in all samples.
Library preparation was performed according to the manufacturer’s instructions for the 10× Chromium single-cell kit (10x Genomics). The libraries were then pooled and sequenced on four lanes on a NextSeq500 sequencer (Illumina).

value: Submandibular gland

tag: strain

value: ICR

value: Wid type

value: control


title: set2D, H3K364tU, Rep2, H3K36

description: 4tU-labled RNA

source_name: MATα his3Δ200 set2∆::KANMX


title: Plasma miRNA-seq at ET11 of CP YFC-90 [YFC-90-2]

tag: sample type

value: plasma


title: iTreg_72h_LIRIL2R_LNA2_rep3


title: Plasma miRNA-seq at ET11 of CP YFC-135 [YFC-135-2]

tag: bmi

value: morula


title: iTreg_72h_LIRIL2R_LNA2_rep2


title: Plasma miRNA-seq at ET14 of CP YFC-142 [YFC-142-3]

tag: endometrial thickness_at_et

value: blastocyst


title: Plasma miRNA-seq at ET11 of CP YFC-116 [YFC-116-2]

tag: number of_transferred_embryos

value: CP


title: SET2D3, H3K364tU, Rep2, H3K36

description: 4tU-labled RNA

source_name: MATα his3Δ200 SET2∆3


title: E13 Parotid gland mesenchyme

source_name: Parotid gland

value: Parotid gland


title: set2D, H3K364tU, Rep1, H3K36

description: 4tU-labled RNA


title: E13 Parotid gland epithelium


title: Plasma miRNA-seq at ET11 of CP YFC-55 [YFC-55-2]

tag: stage of_transferred_embryos


title: Bulk E13 Submandibular gland mesenchyme, replicate 3

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCm38.vM11+ERCCs murine genome using STAR v2.5.2a in single-pass mode
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a custom GRCm38.vM11+ERCCs genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the EdgeR R package.
Assembly: Custom mm10/GRCm38.vM11+ERCCs
Supplementary files format and content: Raw gene counts in tab-delimited txt format.
Supplementary files format and content: Filtered raw gene counts in tab-delimited txt format, after removal of genes with less that 5 reads in at least 1 sample.
Supplementary files format and content: TMM-normalized annotated gene expression matrix in counts per million reads units, tab-delimited txt format.

source_name: Submandibular Mesenchyme

extract_protocol:
Submandibular salivary glands at embryonic day (E) 13 and parotid glands at E13 were harvested. Four independent biological replicates were collected. The TRIzol RNA isolation method was used (Invitrogen). RNA quantity and integrity were assessed using a 2100 Bioanalyzer (Agilent Technologies). All samples for sequencing had RNA integrity (RIN) values > 8.7.
Total RNA per sample was reverse transcribed, and full-length cDNA was generated using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA). Libraries for Illumina sequencing were prepared using the Nextera XT kit (Illumina), pooled, and analyzed on four lanes of a NextSeq 500 (Illumina).

value: Submandibular Mesenchyme

value: Wild Type


title: Plasma miRNA-seq at ET11 of CP YFC-78 [YFC-78-2]

tag: timing of_sample_collection


title: iTreg_72h_NT_rep4

value: NT LNA


title: iTreg_72h_LIRIL2R_LNA1_rep3

value: LIRIL2R LNA1


title: Bulk E13 Submandibular gland mesenchyme, replicate 2


title: set21261, H3K364tU, Rep2, H3K36

description: 4tU-labled RNA

source_name: MATα his3Δ200 set2(1-216)-13xMYC::KANMX


title: E13 Submandibular gland mesenchyme


title: Bulk E13 Submandibular gland mesenchyme, replicate 4


title: iTreg_72h_LIRIL2R_LNA1_rep4

value: blood


title: set21261, H3K364tU, Rep1, H3K36

description: 4tU-labled RNA


title: Wt, H3K364tU, Rep1, H3K36

description: 4tU-labled RNA


title: Bulk E13 Submandibular gland mesenchyme, replicate 1


title: SET2D3, H3K364tU, Rep1, H3K36

description: 4tU-labled RNA


title: iTreg_72h_NT_rep3

value: CD4+ T cells


title: Plasma miRNA-seq at ET11 of CP YFC-70 [YFC-70-2]

tag: reproductive outcome


title: Plasma miRNA-seq at ET11 of CP YFC-109 [YFC-109-2]

tag: tissue


title: iTreg_72h_LIRIL2R_LNA1_rep2

tag: treatment


title: paf1DSET2D3, H3K364tU, Rep1, H3K36

description: 4tU-labled RNA

source_name: MATα his3Δ200 ura3-52 paf1∆ SET2∆3


title: paf1DSET2D3, H3K364tU, Rep2, H3K36

description: 4tU-labled RNA


title: Bulk E13 Submandibular gland epithelium, replicate 4

source_name: Submandibular Epithelium

value: Submandibular Epithelium

tag: genotype


title: paf1D, H3K364tU, Rep2, H3K36

description: 4tU-labled RNA

source_name: MATα his3Δ200 ura3-52 paf1∆


title: iTreg_72h_NT_rep2

value: Activated under iTreg condition for 72 hours


title: Bulk E13 Submandibular gland epithelium, replicate 3

tag: age


title: Plasma miRNA-seq at ET11 of CP YFC-64 [YFC-64-2]

value: cleavage


title: iTreg_48h_LIRIL2R_LNA2_rep4

value: LIRIL2R LNA2

value: Activated under iTreg condition for 48 hours


title: paf1D, H3K364tU, Rep1, H3K36

description: 4tU-labled RNA


title: Plasma miRNA-seq at ET11 of CP YFC-142 [YFC-142-2]


title: Bulk E13 Submandibular gland epithelium, replicate 1

value: ICR


title: Plasma miRNA-seq at ET0 of CP YFC-90 [YFC-90-1]

value: plasma


title: Bulk E13 Parotid gland mesenchyme, replicate 4

source_name: Parotid Mesenchyme

value: Parotid Mesenchyme


title: Wtos, Veh, Rep2, Paf1CAID

description: 4tU-labled RNA

source_name: MATa his3Δ200::HIS3-osTIR lys2-128δ leu2Δ1 ura3-55


title: iTreg_48h_LIRIL2R_LNA2_rep2


title: Plasma miRNA-seq at ET0 of CP YFC-135 [YFC-135-1]

value: morula


title: Wtos, Veh, Rep1, Paf1CAID

description: 4tU-labled RNA

source_name: MATa his3Δ200::HIS3-osTIR lys2-128δ leu2Δ1 ura3-54


title: Plasma miRNA-seq at ET11 of CP YFC-74 [YFC-74-2]

value: CP


title: Bulk E13 Parotid gland mesenchyme, replicate 3


title: iTreg_48h_LIRIL2R_LNA1_rep4


title: Bulk E13 Parotid gland mesenchyme, replicate 2


title: iTreg_48h_LIRIL2R_LNA1_rep2


title: Plasma miRNA-seq at ET0 of CP YFC-116 [YFC-116-1]

value: blastocyst


title: iTreg_48h_LIRIL2R_LNA1_rep3


title: Plasma miRNA-seq at ET0 of CP YFC-78 [YFC-78-1]


title: Bulk E13 Parotid gland epithelium, replicate 4

source_name: Parotid Epithelium

value: Parotid Epithelium


title: Plasma miRNA-seq at ET0 of CP YFC-55 [YFC-55-1]


title: Wtos, Aux, Rep2, Paf1CAID

description: 4tU-labled RNA

source_name: MATa his3Δ200::HIS3-osTIR lys2-128δ leu2Δ1 ura3-53

value: 1:1000 v/v 0.5 M Auxin in DMSO


title: Wtos, Aux, Rep1, Paf1CAID

description: 4tU-labled RNA

source_name: MATa his3Δ200::HIS3-osTIR lys2-128δ leu2Δ1 ura3-52


title: iTreg_48h_NT_rep4

value: NT LNA


title: Plasma miRNA-seq at ET0 of CP YFC-70 [YFC-70-1]


title: Bulk E13 Parotid gland epithelium, replicate 3

value: Wild Type


title: iTreg_48h_NT_rep3

value: blood


title: Bulk E13 Submandibular gland epithelium, replicate 2


title: Bulk E13 Parotid gland mesenchyme, replicate 1


title: Rtf1, Veh, Rep2, Paf1CAID

description: 4tU-labled RNA

source_name: MATa his3Δ200::HIS3-osTIR lys2-128δ leu2Δ ura3-52 RTF1-V5-IAA7(AID)::KANMX


title: Rtf1, Veh, Rep1, Paf1CAID

description: 4tU-labled RNA


title: iTreg_48h_LIRIL2R_LNA2_rep3

source_name: blood

value: CD4+ T cells


title: Plasma miRNA-seq at ET0 of CP YFC-109 [YFC-109-1]


title: iTreg_48h_NT_rep2


title: Plasma miRNA-seq at ET0 of CP YFC-74 [YFC-74-1]


title: Rtf1, Aux, Rep1, Paf1CAID

description: 4tU-labled RNA


title: Bulk E13 Parotid gland epithelium, replicate 1


title: iTreg_24h_LIRIL2R_LNA2_rep3_lane8

value: Activated under iTreg condition for 24 hours


title: Paf1, Veh, Rep2, Paf1CAID

description: 4tU-labled RNA

source_name: MATa his3Δ200::HIS3-osTIR lys2-128δ leu2Δ1 ura3-52 PAF1-V5-IAA7(AID)::KANMX


title: Plasma miRNA-seq at ET0 of CP YFC-64 [YFC-64-1]


title: SJNBL030721_X3, single-nucleus

city: Memphis

first: Michael

last: Dyer

state: TN

address: 262 Danny Thomas Pl MS 324

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1 (10x Genomics).
Assembly: GRCh38-and-mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism:
Homo sapiens
Mus musculus

source_name: Neuroblastoma O-PDX

extract_protocol:
For single-cell RNA-seq, fresh samples were dissociated using the Worthington papain dissociation method (dx.doi.org/10.17504/protocols.io.98ah9se). For single-nucleus RNA-seq, flash frozen samples were dissociated using TST buffer (dx.doi.org/10.17504/protocols.io.bhbcj2iw)
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

value: Neuroblastoma O-PDX

tag: gender

value: M

tag: inss stage

tag: mycn

value: amplified

tag: diagnostic or_recurrence

value: diagnostic

tag: tissue type

value: primary


title: iTreg_24h_LIRIL2R_LNA2_rep3_lane7

tag: cell type

value: LIRIL2R LNA2


title: SJNBL030721_X2, single-nucleus

description: 10x Genomics


title: SJNBL030721_X1, single-nucleus

description: 10x Genomics


title: Plasma miRNA-seq at ET14 of BP YFC-17 [YFC-17-3]

tag: sample type

value: plasma

value: BPL


title: Plasma miRNA-seq at ET0 of CP YFC-142 [YFC-142-1]

tag: bmi

value: CP


title: Paf1, Aux, Rep2, Paf1CAID

description: 4tU-labled RNA

tag: cell line

tag: time (minutes)


title: Plasma miRNA-seq at ET14 of BP YFC-130 [YFC-130-3]

tag: endometrial thickness_at_et

tag: number of_transferred_embryos

tag: stage of_transferred_embryos

value: morula


title: iTreg_24h_LIRIL2R_LNA2_rep1_lane8

tag: tissue


title: iTreg_24h_LIRIL2R_LNA2_rep2_lane7

tag: treatment


title: SJNBL030339_X1, single-nucleus

description: 10x Genomics

value: non-amplified


title: Paf1, Veh, Rep1, Paf1CAID

description: 4tU-labled RNA


title: SJNBL030513_X1, single-nucleus

description: 10x Genomics

value: F


title: iTreg_24h_LIRIL2R_LNA2_rep1_lane7

tag: genotype


title: Paf1, Aux, Rep1, Paf1CAID

description: 4tU-labled RNA

value: 1:1000 v/v 0.5 M Auxin in DMSO


title: Plasma miRNA-seq at ET14 of BP YFC-120 [YFC-120-3]

tag: age

tag: timing of_sample_collection

tag: reproductive outcome


title: Rtf1, Aux, Rep2, Paf1CAID

description: 4tU-labled RNA


title: Leo1, Veh, Rep1, Paf1CAID

description: 4tU-labled RNA

source_name: MATa his3Δ200::HIS3-osTIR lys2-128δ leu2Δ1 ura3-52 LEO1-V5-IAA7(AID)::KANMX


title: Plasma miRNA-seq at ET14 of BP YFC-105 [YFC-105-3]


title: Bulk E13 Parotid gland epithelium, replicate 2

value: Parotid Epithelium

tag: strain

value: ICR

value: Wild Type


title: SJNBL063821_X1, single-nucleus

description: 10x Genomics

tag: gender

tag: inss stage

tag: mycn

tag: diagnostic or_recurrence


title: Leo1, Aux, Rep2, Paf1CAID

description: 4tU-labled RNA


title: Leo1, Veh, Rep2, Paf1CAID

description: 4tU-labled RNA


title: Plasma miRNA-seq at ET14 of BP YFC-83 [YFC-83-3]

value: blood

tag: sample type

tag: bmi

value: blastocyst


title: iTreg_24h_LIRIL2R_LNA1_rep3_lane7

tag: cell type

value: CD4+ T cells

value: LIRIL2R LNA1

value: Activated under iTreg condition for 24 hours


title: Leo1, Aux, Rep1, Paf1CAID

description: 4tU-labled RNA

tag: cell line

tag: time (minutes)


title: iTreg_24h_LIRIL2R_LNA2_rep2_lane8


title: SJNBL063820_X1, single-nucleus

description: 10x Genomics

value: Neuroblastoma O-PDX

value: amplified

value: diagnostic

tag: tissue type

value: primary


title: Plasma miRNA-seq at ET14 of BP YFC-36 [YFC-36-3]

tag: tissue

value: plasma

tag: endometrial thickness_at_et

tag: number of_transferred_embryos

tag: stage of_transferred_embryos

value: cleavage

value: BPL


title: iTreg_24h_LIRIL2R_LNA1_rep2_lane8

tag: genotype

tag: treatment


title: Plasma miRNA-seq at ET14 of BP YFC-26 [YFC-26-3]

tag: age

tag: timing of_sample_collection

tag: reproductive outcome


title: SJNBL047443_X1, single-nucleus

description: 10x Genomics

tag: gender

value: M

tag: mycn

value: non-amplified

value: recurrence

value: metastasis


title: Plasma miRNA-seq at ET14 of BP YFC-10 [YFC-10-3]

tag: sample type


title: iTreg_24h_LIRIL2R_LNA1_rep2_lane7


title: Ctr9, Veh, Rep2, Paf1CAID

description: 4tU-labled RNA

source_name: MATa his3Δ200::HIS3-osTIR lys2-128δ leu2Δ1 ura3-52 CTR9-V5-IAA7(AID)::KANMX


title: Ctr9, Veh, Rep1, Paf1CAID

description: 4tU-labled RNA


title: SJNBL046148_X1, single-nucleus

description: 10x Genomics

tag: inss stage

tag: diagnostic or_recurrence


title: iTreg_24h_LIRIL2R_LNA1_rep1_lane8

tag: cell type


title: SJNBL046145_X1, single-nucleus

description: 10x Genomics

value: F


title: iTreg_24h_LIRIL2R_LNA1_rep1_lane7

value: blood


title: Plasma miRNA-seq at ET11 of BP YFC-32 [YFC-32-2]

tag: bmi

value: blastocyst


title: iTreg_24h_LIRIL2R_LNA1_rep3_lane8

value: CD4+ T cells


title: Ctr9, Aux, Rep2, Paf1CAID

description: 4tU-labled RNA

tag: cell line

value: 1:1000 v/v 0.5 M Auxin in DMSO

tag: time (minutes)


title: Plasma miRNA-seq at ET11 of BP YFC-28 [YFC-28-2]

tag: tissue

tag: endometrial thickness_at_et


title: Ctr9, Aux, Rep1, Paf1CAID

description: 4tU-labled RNA


title: SJNBL013763_X1, single-nucleus

description: 10x Genomics

tag: tissue type


title: iTreg_24h_NT_rep3_lane8

tag: genotype

value: NT LNA

value: Activated under iTreg condition for 24 hours


title: Plasma miRNA-seq at ET11 of BP YFC-17 [YFC-17-2]

tag: number of_transferred_embryos

tag: stage of_transferred_embryos

value: morula


title: SJNBL015724_X1, single-nucleus

description: 10x Genomics

value: Neuroblastoma O-PDX

tag: age

value: diagnostic


title: Cdc73, Veh, Rep2, Paf1CAID

description: 4tU-labled RNA

source_name: MATa his3Δ200::HIS3-osTIR lys2-128δ leu2Δ1 ura3-52 CDC73-V5-IAA7(AID)::KANMX

tag: treatment


title: iTreg_24h_NT_rep3_lane7


title: SJNBL108_X, single-nucleus

description: 10x Genomics

tag: gender

value: primary


title: iTreg_24h_NT_rep2_lane8


title: Cdc73, Veh, Rep1, Paf1CAID

description: 4tU-labled RNA


title: Plasma miRNA-seq at ET11 of BP YFC-120 [YFC-120-2]

value: plasma

tag: timing of_sample_collection

tag: reproductive outcome


title: Cdc73, Aux, Rep2, Paf1CAID

description: 4tU-labled RNA


title: SJNBL046_X, single-nucleus

description: 10x Genomics

tag: inss stage

tag: mycn

value: amplified


title: iTreg_24h_NT_rep2_lane7

tag: cell type


title: Cdc73, Aux, Rep1, Paf1CAID

description: 4tU-labled RNA


title: iTreg_24h_NT_rep1_lane8


title: Plasma miRNA-seq at ET11 of BP YFC-105 [YFC-105-2]

tag: sample type

tag: bmi

value: BPL


title: Plasma miRNA-seq at ET11 of BP YFC-83 [YFC-83-2]


title: Wt, 4tU, Rep2, Paf1CD

description: 4tU-labled RNA

source_name: MATa his4-912δ lys2-128δ leu2Δ1 trp1Δ63

tag: cell line

tag: time (minutes)


title: Wt, 4tU, Rep2, B2-Paf1CD

description: 4tU-labled RNA


title: iTreg_24h_NT_rep1_lane7

tag: tissue


title: Plasma miRNA-seq at ET11 of BP YFC-36 [YFC-36-2]

tag: endometrial thickness_at_et

value: cleavage


title: SJNBL012407_X1, single-nucleus

description: 10x Genomics

tag: diagnostic or_recurrence

tag: tissue type


title: Plasma miRNA-seq at ET11 of BP YFC-10 [YFC-10-2]

tag: number of_transferred_embryos

tag: stage of_transferred_embryos


title: Plasma miRNA-seq at ET11 of BP YFC-26 [YFC-26-2]

tag: age


title: Wt, 4tU, Rep1, B2-Paf1CD

description: 4tU-labled RNA

tag: treatment


title: Gentamicin 20 min, input DNA

city: Beijing

first: Ruochen

last: Chai

address: Haidian District

institute: Tsinghua University

data_processing:
We performed the same steps as before, including quality control, adapter trimming, and sequence alignment. For the ChIP-seq and DNA input control libraries, we used bedtools genomecov with the '-pc' option to calculate the coverage at each nucleotide position, and normalize it to reads per million. To reduce noise, we excluded positions with coverage less than 5. Finally, we divided the read counts at each nucleotide position in the ChIP-seq data by the read counts at the corresponding position in the input DNA control, yielding the ChIP-seq signal of RpoB and Gam. To perform Gam peak calling, we filtered for candidate regions based on the following criteria: Normalized coverage per nucleotide ≥ 1.3, and the region width ≥ 250 bp. Then, all peak locations in each library was compiled into a BED file. Finally, we merged the filtered lists from all four time points (0 minutes, 20 minutes, 40 minutes, and 60 minutes) by bedtools merge (v2.30.0) with default parameters, and generated a final set of 355 Gam peak locations.
Assembly: NC_000913.3
Supplementary files format and content: txt file for coevrage per base and bed file for peak annotation.

organism: Escherichia coli

source_name: BW25113 lacYI::lacIAM-Ptac-gam-3xFLAG

growth_protocol: The overnight seed culture of BW25113 lacYI::lacIAM-Ptac-gam-3xFLAG was diluted 1:350 with fresh LB medium. When the culture grew to OD600~0.4, it was further diluted 1:50 into 200 ml of LB supplemented with 80 μM IPTG (Sigma, V900917). Once the culture reached an OD600 of 0.5, a 40 ml culture was taken as the 0 min sample.

extract_protocol:
The Cells were harvest by spin at 5,000 g for 3 min, and washed once with 20 ml PBS. The washed cell pellets were then resuspended in 1% paraformaldehyde (Beyotime, P0099) diluted by PBS (5 ml for 40 ml culture of OD600~0.5, with the volume adjusted accordingly), and incubated at 25 °C for 30 min with rotation to perform crosslinking. The fixation reaction was quenched by adding Glycine-HCl (Solarbio, G8200; Sigma, 320331) solution to a final concentration of 125 mM. The fixed cells were collected and washed twice with 10 ml TBS (50 mM Tris HCl, 150 mM NaCl, pH 7.4), and then frozen by liquid nitrogen and stored at -80 °C before use. The thawed pellets were resuspended with 1.1 ml TBS supplemented with proteinase inhibitor (Thermo Fisher, A32955), and sonicated on ice until the resuspensions turned clear. After spin at 12,000 g for 10 min, the supernatant of lysates was transferred to a new tube. Each lysate was split into a DNA input control (0.1 ml) and immunoprecipitation (IP) samples for Gam-3xFLAG ChIP (0.5 ml) and RpoB ChIP (0.5 ml). For the RpoB ChIP experiments, 8 μl of anti-RpoB antibody (Abcam, ab191598) was added to the IP lysate and incubated overnight at 4 °C with rotation. Next, 20 μl of Dynabeads Protein G (Thermo Fisher, 10003D) were added to the IP-RpoB lysate and incubated for 3 h at 4 °C with rotation. The beads were pelleted using a magnetic rack, and washed three times with 0.2 ml of TBS. During the last wash, the resuspension was transferred to a new tube before discarding the supernatant. Elution was performed by resuspending the washed beads in 70 ml of 50 mM Glycine-HCl (pH 2.8). After a 2-min incubation, the eluate was carefully collected. The elution was performed twice, and the eluates were combined. Finally, 15 μl of 1M Tris (pH 8.0) was then added to neutralize the pH. For the Gam-3xFLAG ChIP experiments, 20 μl ANTI-FLAG M2 magnetic beads (Sigma, M8823) were added to another IP lysate and incubated for 2 h at 4 °C with rotation. The beads were then washed and eluted as stated in the RpoB ChIP experiment.  Together with the DNA input control, we incubated the eluates from RpoB ChIP and Gam-3xFLAG ChIP at 65 °C overnight with mild shaking, supplementing with Proteinase K at a final concentration of 0.4 mg/ml. We then extracted the DNA from those samples using the MasterPure Complete DNA/RNA Purification Kit, and measured the concentration with the Qubit 1xdsDNA HS Assay Kit.
For library construction, we used the same process as described in the genome re-sequencing, but input 5 ng DNA per sample and scaled down the tagmentation system accordingly.

treatment_protocol: Gentamicin was then added to the remaining culture to a final concentration of 6 μg/ml and mixed thoroughly.

value: BW25113 lacYI::lacIAM-Ptac-gam-3xFLAG

value: 6 mg/L, gentamicin


title: Wt, 4tU, Rep1, Paf1CD

description: 4tU-labled RNA


title: 0 min, input DNA


title: Gentamicin 60 min, input DNA


title: Gentamicin 40 min, input DNA


title: Plasma miRNA-seq at ET0 of BP YFC-32 [YFC-32-1]

tag: timing of_sample_collection


title: Plasma miRNA-seq at ET11 of BP YFC-130 [YFC-130-2]

tag: reproductive outcome


title: rtf1D, 4tU, Rep2, B2-Paf1CD

description: 4tU-labled RNA

source_name: MATα his4-912δ lys2-128δ leu2Δ1 trp1Δ63 rtf1Δ::KANMX


title: Plasma miRNA-seq at ET0 of BP YFC-28 [YFC-28-1]


title: rtf1D, 4tU, Rep1, B2-Paf1CD

description: 4tU-labled RNA


title: paf1D, 4tU, Rep2, Paf1CD

description: 4tU-labled RNA

source_name: MATα his4-912δ lys2-128δ leu2Δ1 trp1Δ63 paf1Δ::KANMX


title: Gentamicin 60 min, Gam-3xFLAG ChIP-seq


title: Plasma miRNA-seq at ET0 of BP YFC-17 [YFC-17-1]


title: Gentamicin 40 min, Gam-3xFLAG ChIP-seq


title: SJNBL031239_D1, single-cell

description: 10x Genomics

tag: gender

value: F

tag: inss stage


title: paf1D, 4tU, Rep1, Paf1CD

description: 4tU-labled RNA


title: leo1D, 4tU, Rep2, Paf1CD

description: 4tU-labled RNA

source_name: MATa his4-912δ lys2-128δ ura3-52 trp1Δ63 leo1Δ::KanMX


title: SJNBL046_X, single-cell

description: 10x Genomics

value: M

tag: mycn


title: Gentamicin 20 min, Gam-3xFLAG ChIP-seq


title: 0 min, Gam-3xFLAG ChIP-seq


title: Plasma miRNA-seq at ET0 of BP YFC-105 [YFC-105-1]

value: blood

tag: sample type


title: leo1D, 4tU, Rep1, Paf1CD

description: 4tU-labled RNA


title: Gentamicin 60 min, RpoB ChIP-seq


title: Plasma miRNA-seq at ET0 of BP YFC-83 [YFC-83-1]

tag: bmi

value: blastocyst


title: Gentamicin 40 min, RpoB ChIP-seq

tag: cell line


title: ctr9D, 4tU, Rep1, Paf1CD

description: 4tU-labled RNA

source_name: MATα his4-912δ lys2-128δ trp1Δ63 ctr9Δ::KANMX

tag: time (minutes)


title: Plasma miRNA-seq at ET0 of BP YFC-36 [YFC-36-1]

tag: tissue


title: Plasma miRNA-seq at ET0 of BP YFC-26 [YFC-26-1]

tag: endometrial thickness_at_et


title: cdc73D, 4tU, Rep2, Paf1CD

description: 4tU-labled RNA

source_name: MATa his4-912δ lys2-128δ trp1Δ63 cdc73Δ::KANMX


title: cdc73D, 4tU, Rep1, Paf1CD

description: 4tU-labled RNA


title: ctr9D, 4tU, Rep2, Paf1CD

description: 4tU-labled RNA


title: Plasma miRNA-seq at ET0 of BP YFC-10 [YFC-10-1]


title: NEB, total, testis, b3

status: Public on May 14 2024

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
For LIDAR, LIDAR3 and NEB samples: Adapter trimming with TrimGalore v0.6.4: --length 5 --paired --retain_unpaired -r 20 -r 100. For NEB samples, additional trimming step with Cutadapt v 4.2: cutadapt -A GATCGTCGG --minimum-length 5 --paired-filter any
Samples with UMI (LIDAR, LIDAR-3): UMIs were extracted using umi_tools v1.1.2 with the regex ".*(?<umi_1>.{7})CG(?P<umi_2>.{2})AG(?P<umi_3>.{2})GGG" and remaining constant bases were trimmed with Cutadapt (cutadapt --minimum-length 5 -g CGAGGGG), then TSO dimers were removed with Cutadapt (cutadapt -e 3 -b CGTCAGATGTGTATAAGAGACAG --discard-trimmed)
Reads were mapped sequentially with STAR v2.7.10a to consensus rRNA repeats (BK000964.3), snoRNA from GENCODE vM27, snRNA from GENCODE vM27, piRNA from piRbase v3.0 using bowtie2 ver2.5.0, and tRNA from GtRNAdb and tRNAscan-SE as curated by Nedialkova et al. using GSNAP ver 2019-02-26 with SNP database provided, then to a custom GRCm39 genome with all of the sequences above masked and provided as extra scaffolds, using STAR (paired reads with inserts > 100nt) or bowtie2 (paired reads with inserts < 100nt and single reads)
Samples with UMI (LIDAR, LIDAR-3): bam files were deduplicated using umi_tools dedup with method --unique
Only reads with fragment length >=15 were retained for downstream analysis
Assembly: GRCm39
Supplementary files format and content: tab delimited files include raw counts corresponding to each gene (counts.genes.txt) or biotype, including reads mapped to non-annotation regions (counts.biotypes.txt)

source_name: mouse testis

extract_protocol:
LIDAR and LIDAR-3 library preparation: The desired amount of total and fractionated RNAs was diluted to 1μl and mixed with 0.4μl of 10μM LIDAR_RT_primer (/5Biosg/GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGNNNNND). To anneal the LIDAR_RT_primer to the template RNA, samples were heated to 65°C for 5 min, then temperature was lowered to 4°C (0.5°C/s). To initiate retrotranscription, 6.28μl of RT_mix [25mM Tris-HCl pH=8.3, 20mM NaCl, 2.5mM MgCl2, 8mM DTT, 5% PEG-8000, 0.5mM dNTPs, 1mM GTP, 0.5 U/μl Murine RNase inhibitor, and 2U/μl Maxima H-minus Reverse Transcriptase – concentrations refer to a final volume of 8 μl] were added and samples were incubated at 25°C for 10 min. To further promote cDNA synthesis and template switch, temperature was raised to 42°C, 0.32μl of 50μM LIDAR_TSO_mix (equimolar ratio of the following oligos: /5Biosg/CGTCAGATGTGTATAAGAGACAGtgNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhgNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhtgNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhmtgNNcgNNagNNrGrGrG) were added, and samples were incubated at 42°C for 80 min, followed by 10 cycles at 50°C for 2 min and 42°C for 2 min, then at 85°C for 5 min. To pre-amplify and add adapters to cDNA, 12μl of KAPA_mix [1X KAPA HiFi HotStart buffer Ready Mix, 0.5μM LIDAR_preamp_f (TCGTCGGCAGCGTCAGATGTGTATAAGAGAC*A*G), and 0.1μM LIDAR_preamp_r (GTCTCGTGGGCTCGGAGA) – concentrations refer to a final volume of 20 μl]  were added and samples were incubated with the following PCR cycling conditions: denaturation (95°C for 3 min), 18 cycles of amplification (98°C for 20s, 70°C for 30s, 72°C for 30s), final extension (72°C for 5 min). Quality of adapter-containing libraries was assessed by loading 5ul on a 2% agarose gel. To generate the final libraries, 2μl of pre-amplified were diluted to 37μl with 10mM Tris-HCl pH=8, 0.5μl of each 10μM custom Nextera indexing primers was added, followed by 12μl of Q5_mix [1X Q5 buffer, 0.5mM dNTPs, 0.02 U/µl Q5 High-Fidelity DNA Polymerase (Cat. No M0491, New England Biolabs) – concentrations refer to a final volume of 50 μl]. Samples were incubated with the following PCR cycling conditions: denaturation (98°C for 30 sec), 18 cycles of amplification (98°C for 10s, 65°C for 20s, 72°C for 20s), final extension (72°C for 2 min). Indexed libraries were purified using 2.3X SPRI beads and eluted in 50μl of TE buffer (10mM Tris-HCl pH=8, 1mM EDTA).
For LIDAR-3, the LIDAR-3_RT_oligo was generated by mixing equimolar amounts of LIDAR-3_RT_sense (/5Biosg/GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGNNNNNN) and LIDAR-3_RT_antisense (CdUGdUCdUCdUdUAdUACACAdUCdUCCGAG/3ddC/), followed by heating at 95°C for 5 min, and a slow cool down to 25°C (0.1°C/s). To prepare LIDARsp libraries, 1μl of input RNA was first denatured at 70°C for 2 min, then temperature was lowered to 50°C and 0.4μl of 1μM LIDAR-3_RT_oligo were added. Samples were incubated at 50°C for further 2min, then temperature was lowered to 4°C (0.5°C/s). To initiate retrotranscription, 6.28μl of RT_mix were added and samples were incubated at 25°C for 10 min. To further promote cDNA synthesis and template switch, temperature was raised to 42°C, 0.32μl of 50μM LIDAR_TSO_mix were added, and samples were incubated at 50°C for 80 min, followed by 10 cycles at 55°C for 2 min and 50°C for 2 min, then at 85°C for 5 min. LIDAR-3_RT_antisense was digested by adding 1ul of USER II enzyme and incubating at 37°C for 30 min. USER II was heat inactivated by incubation at 65°C for 10 min. To pre-amplify and add adapters to cDNA, 12μl of KAPAsp_mix [1X KAPA HiFi HotStart buffer Ready Mix, 2μM LIDAR_preamp_f (TCGTCGGCAGCGTCAGATGTGTATAAGAGAC*A*G), and 0.5μM LIDAR_preamp_r (GTCTCGTGGGCTCGGAGA) – concentrations refer to a final volume of 20 μl] were added and samples were incubated with the following PCR cycling conditions: denaturation (95°C for 3 min), 6 cycles of 3-step amplification (98°C for 20s, 63°C for 30s, 72°C for 30s), 12 cycles of 2-step amplification (98°C for 20s, 72°C for 50s), final extension (72°C for 5 min). Quality of adapter-containing libraries was assessed by loading 5ul on a 2% agarose gel. To generate the final libraries, 2μl of pre-amplified were diluted to 37μl with 10mM Tris-HCl pH=8, 1μl of each 10μM custom Nextera indexing primers was added, followed by 12μl of Q5sp_mix [1X Q5 buffer, 0.5mM dNTPs, 0.02 U/µl Q5 High-Fidelity DNA Polymerase – concentrations refer to a final volume of 50 μl]. Samples were incubated with the following PCR cycling conditions: denaturation (98°C for 30 sec), 7 cycles of amplification (98°C for 10s, 65°C for 20s, 72°C for 20s), final extension (72°C for 5 min). Indexed libraries were purified using 2.4X SPRI beads and eluted in 50μl of TE buffer (10mM Tris-HCl pH=8, 1mM EDTA).
Small RNA-seq and mRNA-seq library preparation
Small RNA libraries were prepared using the NEBnext Small RNA Library Prep Set for Illumina (Cat. No E7330S, New England Biolabs), following the standard protocol with the following parameters: 1) 1:2 dilution of 3’SR Adaptor, SR RT Primer, and 5’SR Adaptor 2) 15 indexing PCR cycles 3) cleanup of final libraries with QIAgen MinElute PCR purification kit, followed by a second cleanup with 2X SPRI. Libraries were analyzed on a 6% non-denaturing polyacrylamide gel.
For mRNA-seq libraries, polyA RNA was enriched from 2 μg total RNA using Dynabeads Oligo(dT)25. Poly-A-enriched fraction was used for library construction using the NEBnext Ultra II Directional Library Prep Kit for Illumina (Cat. No. E7760L, New England Biolabs), following the standard protocol but using half the reaction volumes recommended. Libraries were analyzed on a 2% agarose gel.
Both small RNA-seq and mRNA-seq libraries were quantified using NEBNext Library Quant Kit for Illumina (Cat. No E7630L, New England Biolabs). Libraries were sequenced on an Illumina NextSeq500 instrument.

treatment_protocol: C57BL/6 mouse embryonic stem cells (ESC) were purchased from ATCC (SCRC-1002) and maintained onto 1% gelatin-coated dishes in DMEM knockout medium supplemented with 15% ES-grade Fetal Bovine Serum, 1% GlutaMAX, 1% Non-essential aminoacids, 0.5% Penicillin/Streptomycin solution, 110μM β-mercaptoethanol, 100 units/ml Leukemia Inhibitory Factor (LIF), 3μM GSK-3 Inhibitor XVI, 1 μM MEK1/2 Inhibitor III. Cells were passaged through trypsinization (0.05%) every 2–3 days. Prior to neuronal progenitor cells (NPC) differentiation, embryonic stem cells that were maintained in N2B27 serum-free medium consisting of 1:1 mix of Neurobasal medium and DMEM/F12, supplemented with 1X N2, 1X B27, 1% GlutaMAX, 1% Non-essential aminoacids, 0.5% Penicillin/Streptomycin, 55μM β-mercaptoethanol, 100 units/ml Leukemia Inhibitory Factor (LIF), 3μM GSK-3 Inhibitor XVI, 1 μM MEK1/2 Inhibitor III. For NPC differentiation differentiation, Epiblast-like cells (EpiLC) were induced from ESC in N2B27 serum-free medium (without 2i and LIF) supplemented with 40μg/ml of BSA, and 10ng/ml bFGF for 72h. EpiLC were treated with 500nM SAG in N2B27 serum-free medium (without 2i and LIF) for 48h to generate NPC.

value: mouse testis

tag: input amount_(ng)


title: NEB, total, testis, b1


title: NEB, total, testis, b2


title: NEB, total, brain, b2

source_name: mouse brain

value: mouse brain


title: LIDAR, total, testis, b3


title: NEB, total, brain, b1


title: Plasma miRNA-seq at ET0 of BP YFC-130 [YFC-130-1]


title: LIDAR, total, testis, b2